Sexual systems have profound impacts on genome diversity and structure and they also affect the levels of intragenomic conflict. Tadpole shrimps are rare examples where three sexual systems representing a range of inbreeding occur. Closely related populations of the European tadpole shrimp, Triops cancriformis, can be gonochoric, hermaphroditic or androdioecious (AD, hermaphrodites and rare males). Having previously established that this unique animal system has genetic sex determination, we focused on building up genomic resources in order to assess the impact of different sexual systems on genomes, and sex chromosomes. We have sequenced, assembled and annotated three genomes (male, female hermaphrodite). We also used RADseq to survey the genomic diversity of populations with different sexual systems and characterise sex chromosome structure, differentiation and gene content. We used paired-end RAD sequence data on 47 individuals and the genome assemblies to identify sex chromosome contigs, generate haplotypes and reconstruct the relationships between the sex chromosomes of gonochoric and androdioecious European populations of Triops cancriformis. The genome of T. cancriformis is small, 115-135 Mbp. As expected, hermaphrodite populations have virtually homozygous genomes. We identify 79 putative sex linked genetic markers and 18 sex-linked genomic regions shared by both populations. Triops sex chromosomes are most likely homomorphic. The AD population has a smaller non-recombining region than the gonochoric one, as expected if recombination had increased under androdioecy. Our results establish T. cancriformis is a unique system in which to investigate the genomic impacts of sexual system.