Euphilotes ancilla purpura and cryptica (Lycaenidae), butterflies endemic to the Spring Mountains (Clark Co., Nevada), have been described as two univoltine, temporally isolated, sympatric taxa that utilize different early- and late-flowering larval host plant varieties (Eriogonum umbellatum). However, our results from field and laboratory indicate that this is not the case. The subspecies overlap in timing of adult reproductive flight (compilation of field records 1977 to 2018) and laboratory emergence of adults from early-season, non-diapause pupae indicate butterflies are not univoltine. Genetic samples collected from putative E. a. purpura (Early cohort) and cryptica (Late cohort) subpopulations show no evidence of genetic structure indicative of allochronic isolation in phylogenies of 26 mitochondrial DNA COI haplotypes and 18 nuclear ITS1 alleles. Analysis of molecular variance revealed 89% of mitochondrial DNA variation structured within and among subpopulations, with only 11% between the purportedly isolated subspecies. Analysis of isolation and migration indicated gene flow from the Early to Late cohort was 3 × greater than in the opposite direction. We conclude that, rather than two separate subspecies, Euphilotes ancilla exists in a network of partially interconnected subpopulations extending from 1750 to 3000 m across much of the Spring Mountains. Gene flow is related to the timing of adult flight and host plant flowering, contributing to the genetic variation in phenology necessary for evolutionary tracking of shifting flowering periods of larval host plants. Maintenance of connectivity and gene flow across the Spring Mountains is therefore essential for population persistence of both cohorts in the face of environmental change.