Model experimental organisms are often defined by genotype when researchers establish a consortium of well-characterized laboratory stocks. The hermaphroditic Mangrove Killifish, Kryptolebias marmoratus, is an emerging model species most recognized for its peculiar method of reproduction: self-fertilization. This reproductive mode, unique among all vertebrate animals, has facilitated the establishment of distinct inbred "clonal" lineages that originated from the wild and have been long maintained in the laboratory. The results presented here define the genetic composition of 21 commonly utilized clonal lines of K. marmoratus from laboratories around the world. Evidence is also presented that some microsatellite alleles arose de novo during the laboratory breeding of these lineages and that other such alleles probably segregated from polymorphic ancestral conditions in the wild-caught progenitors. These data should help to make K. marmoratus a more valuable consortium resource for vertebrate research that requires genetically defined clonal lines.