The earliest European presence on Flores was that of the Portuguese, who established missions around the contemporary town of Larantuka at the eastern end of Flores and on the islands of Adonara and Solor.  Not long afterward, at least seven Portuguese mission stations were established on the island of Ende and on the coast of Ende Bay.  Between Larantuka and Ende, the Portuguese presence was sparser, but Visser (1925: 292) locates two stations on the north coast of central Flores, at Dondo on the western end of Maumere Bay and at ‘Krove’ on the north coast near contemporary Nebé.  According to Visser, the station at Krowé was founded between the years 1561 and 1575.
In addition, Visser cites evidence that Paga in the south-western reaches of Kabupaten Sikka and Sikka Natar itself were the sites of such stations on the south coast. While there is only a vague tradition among the contemporary people of Sikka Natar that their village was the site of a Dominican mission station, as Visser reports, it is possible that the village was, if not a Dominican station, then at least a place visited more or less regularly by Dominicans embarked on the Portuguese ships that passed along Flores’s south coast. Visser’s source  identifies the station at Sikka as a ‘parochie’ bearing the name Saint Lucia, and as a congregation numbering 1,000 souls in 1598. 
The earliest mention of Sikka I have found in the literature is that in an unattributed description of the first Christians of the islands of Solor and Timor, which de Sá includes in his compilations of documents from the period 1568-79 relating to the history of Portuguese missions in the Orient:
Map 4: Dominican mission stations on Flores, Adonara and Solor in the 16th century (after Visser 1925: 292)
On this island of Larantuka, there would be fifteen leagues between the main settlement, that is referred to by the same name [i.e., Larantuka], and another that is further ahead on the island, called Siqua [Sikka], and another called Pagua [Paga]. Ende is another fifteen leagues beyond. All are Christian settlements, of one thousand firearms, and the majority, in addition to many other Christians and pagans, are our friends, having the aforesaid weapons. 
Just how frequent and intense was the contact between the Sikkanese and the Dominicans in the 16th and 17th centuries is an important question for which I have no answer. But it is likely that the contacts, and thus the direct influence of the Portuguese on the locals, were mainly on the coasts. Having said this, surely some Portuguese must have ventured inland from time to time (as from Krowé south into Tana ’Ai?) and surely people from the interior must have travelled to the coasts, if only to have a look at the foreigners—no place in east central Flores being more than a day’s walk from the north or the south coasts. Evidence for at least indirect Portuguese influence in the interior is strong. For example, a small number of not-too-mangled Portuguese words turn up in transcriptions of ritual speech I recorded in Tana Wai Brama in the 1970s and 1980s.
The Dutch acquired Flores from the Portuguese in 1859 but it was some years before they became sufficiently interested in the region of Sikka to send a government official there. When that happened in the 1870s, the official settled not in Sikka Natar, the Village of Sikka on the south coast and the home of the rajas, but at Maumere on the north coast. Maumere was then a low-lying, hot, malarial place, sodden in the rainy season and smoky and dusty in the dry. It has since grown into one of the largest towns on Flores, a centre of education, and, with its excellent harbour and landing strip, a major port of entry for Flores and a commercial centre.
According to Dutch records and the hikayat of Kondi and Boer, much shuffling of allegiances and shifting of local negeri (villages, but in the hikayat, clearly the Malay equivalent of tana, ‘domains’) between the two (and for a while, three) rajadoms of Sikka went on in the two centuries before 1925. One effect of the shifting of negeri (each of which was probably a tana with its own tana pu’ang) and the rise of Sikka as a secular polity under the rajas of Sikka was to erode the importance of what the early Dutch records call tana pu’ang-schappen (tana pu’ang-ships). Once this process of incorporation into the rajadom and erosion of the tana pu’angs’ authority was complete—by about 1950—the local tana pu’ang retained respect in their communities, but no longer exercised any real power.
Here we encounter the limitations of the scarce historical sources on the early culture and history of Sikka and a peculiarity of the voluminous later manuscripts written by Sikkanese authors. Briefly, the problem is this: the authors of the first texts written by a few men of the first or second literate generation of Sikkanese were all officials in the government of the Rajadom of Sikka. The two major texts from that era, one by D.D.P. Kondi and the other by A. Boer Pareira, treat the history of Sikka in detail, but from the distinctive point of view of Lepo Geté, the ‘Great House’, the Royal House of Sikka. Since the people of Lepo Geté are, according to their own myth of origin, immigrants to Flores and by no means indigenes, their history cannot be taken to be the history of the indigenous Sikkanese peoples, which remains a subject about which we know very little. Furthermore, even the main outlines of the internal divisions of the Sikkanese people into communities is obscured, firstly by the Dutch, who created the administrative districts of the rajadom, and then by the early Sikkanese authors, who were little concerned with explaining the territorial categories and institutions of the indigenous social landscape but were concerned centrally with the creation of the Sikkanese rajadom and the legitimation of its rule.
Although information about early Dutch activity in Sikka is sketchy at best, we can get at least a general idea of what was going on in the old rajadom between about 1860 and 1942. Indeed, the picture becomes a bit more detailed once the Dutch, with their penchant for archiving the memories van overgave of their officials, arrived in Sikka. 
The Dutch administrative divisions of Flores, which must quickly have become territorial categories in the minds of the Florenese (‘I am of Ende’, ‘He is from Sikka Maumere’, ‘They are Larantukans’), changed often in the years from 1879 until 1942, when the Dutch flag over Flores was replaced briefly with the Japanese rising sun. From 1879 to 1907, these were the administrative divisions of Flores (Map 5):
Note that this was before the Dutch had adjusted administrative boundaries to coincide with the rajadoms they later recognised on the island. Manggarai in the west was part of Gouvernement Celebes en Onderhorigheden (Government of Celebes [Sulawesi] and Dependencies) while the rest of Flores was administratively part of Residentie Timor en Onderhorigheden (Residency of Timor and Dependencies). Within the Residency of Timor, South Flores (Zuid Flores), which included Ende, most of Nage Keo and some of Ngada, was part of the Division (D: Afdeling) of Sumba and Dependencies while the rest of Flores was the Division of Larantuka and Dependencies. Larantuka was divided into the subdivisions or districts (D: Onderafdelingen) of North Flores (which included Sikka and Maumere, which the Dutch had made the administrative centre of the subdivision), East Flores, Solor and Alor. This administrative division of the island did not work too well, as a brief glance at the map might lead us to suspect, and so, in 1907, the lines were redrawn as follows (Map 6):
In these years (1907-09), Manggarai remained part of the Government of Celebes, while the rest of Flores was the Division of Flores and was included in the Residency of Timor. South Flores was removed from the Division of Sumba and made part of the Division of Flores, which was divided into the Subdivisions of South Flores, North Flores, East Flores and the Solor Islands. This arrangement should have worked all right, except that, in 1908, an administrative division between West Flores and East Flores was created. The new division crosscut South Flores and North Flores and must have been the source of innumerable headaches for the officials assigned to the island. But those headaches lasted only two years.
In 1909, the divisions of the island were shuffled once again, in such a way as to bring the administrative divisions into accord with at least some of the rajadoms on the island (Map 7).
Manggarai was removed from the Government of Celebes and made a subdivision (onderafdeling) of the Division of Flores. The old divisions of South Flores, North Flores and East Flores disappeared and were replaced by subdivisions (onderafdelingen) that took greater account, though roughly, of the linguistic, social, economic and, perhaps most important, the political realities of the island. These were (in addition to the Subdivision of Manggarai) the Subdivisions of Ngada (including Nage Keo), Ende (including Lio), Maumere, East Flores (including Larantuka) and the Solor Islands. The subdivisions were further divided into districts (landschappen). Most of the names of the districts corresponded with the names of socio-linguistic groups on the island. The new district and administrative arrangements were comparatively rational, since they took account of the native rajadoms the Dutch had either recognised or created in the previous 50 years. In particular, the three rajadoms of the District of Maumere, Sikka, Nita and Kangae, were clearly demarcated. This arrangement of administrative divisions survived until about 1930, when some of the rajadoms were amalgamated.
Joachim Metzner has given us the following reconstruction of the political divisions of eastern Sikka towards the end of the 19th century. This would have been some 20 years after the earliest entries in the Dagboeken van het Controleuren van Maoemere, which were kept, more or less faithfully, by the posthouders assigned to Maumere, beginning in 1879, but before the dispute between the rajas of Sikka and Larantuka over Tana ’Ai was settled (Map 8). 
Map 8: Political divisions of Sikka towards the end of the 19th century and before Dutch intervention in the border dispute between Sikka and Larantuka
More certain are the political divisions of the District of Maumere after the boundaries established by the Dutch after they settled the Tana ’Ai dispute at the beginning of the 20th century. The settlement placed Tana ’Ai within the Rajadom of Kangae (Map 9).
Here we see plainly the way the Dutch, by 1904, recognised the indigenous polities of the Sikka region, which were ruled by the Raja of Sikka, the Raja of Nita and the Raja of Kangae. The Raja of Kangae ruled a region created by the Dutch when they could find no other way to control the subversive and overtly hostile activities of one Raja Nai against the authority of the Raja of Sikka. These boundaries—around what the Sikkanese called kapitan-schappen—correspond roughly to the kecamatan into which the kabupaten is divided today.
By 1929, the Dutch acceded to the amalgamation of the Rajadoms of Nita and Kangae into the Rajadom of Sikka, whose raja, Mo’ang Ratu Thomas Ximenes da Silva, ruled the whole of the region of Sikka until his death in 1954. The dissolution of the Rajadom of Kangae, which had been born of a rebellion against the Raja of Sikka in the first decade of the 20th century over a question of taxation, followed the enforced settlement by the Dutch of the dispute between the rajas of Sikka and Larantuka over sovereignty over Tana ’Ai, which became firmly part of the Rajadom of Sikka. The Rajadom of Nita, whose rulers were kinsmen of the Raja of Sikka, was also dissolved and its territory placed under the rule of Sikka, partly as an administrative convenience for the Dutch but also in response to the political activity and persuasiveness of Raja Don Thomas, the last of the Sikkanese rulers.
After 1931 and until the beginning of the Japanese occupation in 1942, the administrative map of Flores was as depicted in Map 10: 
These boundaries were those of the rajadoms of Flores within the Division of Flores. Under the government of the newly independent Indonesia, the rajadoms were abolished in the early 1950s, after which the old divisions, and their boundaries, were retained as kabupaten in the new system of government.