Simulium (Simulium) acrotrichum Rubtsov, a black fly from Central Asia, provides a platform for examining the evolutionary relationships of selected species groups in the subgenus Simulium Latreille. The female, male, pupa, and larva of S. acrotrichum are properly associated and morphologically redescribed and illustrated. The banding sequence of the larval polytene chromosomes is compared with that of the Simulium subgeneric standard, from which it differs by nearly 30 fixed rearrangements. Structural and chromosomal features indicate that S. acrotrichum is the sister species of S. flavidum Rubtsov. Simulium acrotrichum can be placed confidently in a group consisting of the S. malyschevi Dorogostaisky, Rubtsov, and Vlasenko and S. reptans (L.) groups, which are part of a larger clade that also includes the S. jenningsi Malloch group. This more inclusive clade is defined chromosomally by a minimum of four fixed inversions, compared with the standard map for the subgenus Simulium. All four inversions are uniquely derived relative to the two selected outgroups, Simulium (Psilozia) vittatum Zetterstedt and Simulium (Boophthora) erythrocephalum (De Geer). The independent monophyly of the S. malyschevi and S. reptans groups, however, cannot be tested without study of additional group members. The problems illustrated by the taxonomic identity and phylogenetic placement of S. acrotrichum argue for an integrated approach to simuliid systematics, drawing from the character stores of morphology, cytology, and molecular biology.