Persistent southwest-to-east aeolian transport occurs in the northern Chihuahuan Desert, crossing multiple ephemeral wetlands. We used the rotifer Euchlanis chihuahuaensis as a model species to investigate potential influence of wind dispersal of diapausing propagules along a directional corridor on its population genetics. A regional aeolian corridor was defined using modeled backward trajectories of 36 years of dust events in the northern Chihuahuan Desert. Molecular data from populations inside and outside of the corridor were analyzed to determine phylogenetic relationships, diversity indices, and population structure. We found population structuring with three haplogroups identified within discrete geographic areas in Southern New Mexico, the Paso Del Norte Region, and Northern Mexico. Evidence of long-range dispersal downwind across the corridor included shared haplotypes from hydrologically disconnected habitats similar to 100 - 230 km apart. Furthermore, haplotype diversity was higher outside of the aeolian corridor, with numerous private and population-specific haplotypes, indicative of reduced connectivity among the populations. Nucleotide diversity for populations within the corridor (0.024) was significantly higher than those outside the corridor (0.012). Comparison of variance partitioning revealed that 16.9% of the genetic variation was among populations when comparing populations from inside to those outside the corridor. We conclude that isolated E. chihuahuaensis populations appear to have continued connectivity in the Chihuahuan Desert, likely mediated by the aeolian corridor which provides routes for gene flow. Understanding how passive dispersal shapes genetic structure for aquatic organisms in arid environments, where habitat fragmentation and climatic variability can severely limit connectivity, has broad implications for conservation strategies and management.