The living fossil Triops cancriformis comprises bisexual (either gonochoric or hermaphroditic) and unisexual populations. Genetic surveys have recently revealed a general trend of low differentiation of 12S and 16S mitochondrial genes. We, therefore, surveyed further mitochondrial (COI gene and control region) and nuclear markers (dinucleotide microsatellites) to assess the genetic variability and to establish any relationship with the different reproductive modes found in European populations. The mitochondrial analyses confirmed the pattern of low variability. Hence, the low mitochondrial genetic variability appears as a common feature of the genus Triops. The microsatellite analysis found that Italian populations are monomorphic or exhibit little polymorphism, while other European samples display a higher degree of polymorphism and private alleles. Spanish, Austrian and Italian populations show patterns of Hardy-Weinberg disequilibrium that could be explained by the mode of reproduction, or by a higher frequency of null alleles in these populations. The low diversity and differentiation among Italian populations lead us to question the Monopolization Hypothesis. One microsatellite locus appears to be sex-linked, with heterozygotes detected only in males and hermaphrodites.