By using cytogenetic analysis of larval polytene chromosomes from small samples of the Simulium arcticum complex of black flies (Diptera: Simuliidae) at the Coeur d'Alene River in northern Idaho in 2004 and 2005 we discovered a population that consisted of individuals having sex chromosomes characteristic of S. saxosum, S. arcticum s. s. and combinations of the two. Most taxa of the S. arcticum complex can be identified only on the basis of their well differentiated sex chromosomes, and the presence of larvae having species specific and combinational sex chromosome types presented us with a unique opportunity to further investigate this rare event. This variety of sex chromosome types could be explained if (1) sex-chromosomes in S. saxosum were operating autosomally in S. arcticum s. s. and vice-versa, (2) the combinational types were formed as a result of hybridization or (3) the population was in genetic equilibrium suggesting a unique entity. The latter possibility could be the remnant of an incipient speciation event. We returned to the Coeur d'Alene in the springs of 2009 and 2010 and made more extensive collections. We analyzed all types present for sex chromosome diversity, frequencies of sex chromosome types, tests of Hardy-Weinberg equilibrium for sex chromosomes and the autosomal polymorphism IS-1, and the extent of chromosome pairing and chromocenter morphology between S. saxosum, S. arcticum s.s. and combinational types. Finally, we analyzed additional larvae of the S. arcticum complex from three sites to the west and four sites to the east of the Coeur d'Alene River to determine the geographic distribution of all types. There is no evidence for alternative sex chromosome types of S. saxosum and S. arcticum s. s. acting autosomally, nor is there evidence for hybridization between S. saxosum and S. arcticum s. s. We therefore conclude that the population at the Coeur d'Alene River may be the remnant of a population that gave rise to S. saxosum to the west and to S. arcticum s. s. to the east. This may be a natural example of a remnant population whose types have experienced “mating trials” of different combinations of sex chromosome types that subsequently gave rise to the described siblings via incipient speciation.