I analyzed larval polytene chromosomes to determine if the hypothesized remnants of an incipient speciation event in the Simulium arcticum complex of black flies previously discovered at the Coeur d'Alene River, Idaho existed elsewhere. This population not only had Y chromosomes that defined two members of the S. arcticum complex: S. arcticum sensu stricto and S. saxosum, but also possessed combinations of sex chromosomes of the two that were in genetic equilibrium with respect to all sex chromosome types. The geographic overlap between S. saxosum to the west and S. arcticum s. s. to the east generally runs north and south of the Coeur d'Alene River. Accordingly, I made 37 additional collections in a north-south orientation during 2011–2013. Larvae from 10 of the 37 collections had sex chromosome types identical to those of the previously studied site at the Coeur d'Alene River, thus expanding the area of putative remnant populations. The St. Joe River not only had Y chromosome combinations identical to those of larvae at the Coeur d'Alene but also had a cytotype new to science based on distinct sex chromosomes (X₀Y_IIL-79) in males. These observations: (1) increase the known geographic area of presumed remnant populations of S. arcticum s. s., of S. saxosum and their combinational types to about 3500 km²; (2) suggest that mating trials still occur; and (3) describe the structure and frequency of inversions in two new cytotypes of the S. arcticum complex.