Anchialine species show restricted geographic ranges, high habitat specificity and small population sizes. These factors make them particularly vulnerable to human activities, yet little is known about their ecology and evolutionary history. Munidopsis polymorpha is a decapod endemic to an anchialine cave system of the Corona lava tube in Lanzarote (Canary Islands). The present study, the first genetic survey conducted on this largely unknown species, was designed to characterize its genetic diversity, population structure and recent demographic history using sequence data for the COI gene and eight microsatellite. A single haplotype was identified in the mitochondrial dataset. Nuclear genetic diversity was also low (average= 4.375 ± 1.685). No significant genetic structure was detected between sampling sites and years, either by AMOVA (FST = 0.006, P= 0.110) or Bayesian clustering analysis (K = 1), indicating this species should be treated as a single management unit. Neither did we find evidence for a recent bottleneck event, and estimates of effective population size were extremely low (∼ 50). The lack of population structure, low genetic diversity and extremely low effective population size reinforces the high degree of isolation and endemicity of this species and consequently the need to implement appropriate management actions.