The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus but overall there is a low rate of outcrossing and therefore, low heterozygosity. In this study, we used whole-genome data to assess the level of genetic diversity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data due to the resolution of full genome sequencing data. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. These data suggest that there is previously undescribed variation within lineages of K. marmoratus. Although this study was limited by the number of lineages that were available, these results highlight the need to sequence additional individuals within and among lineages.