The mangrove killifish (Kryptolebias marmoratus) is the only vertebrate known to be capable of self-fertilization. Its gonad is typically an ovotestis that simultaneously produces eggs and sperm, and fertilization is internal. Although most populations of this species consist primarily or exclusively of hermaphroditic individuals, gonochoristic males occur at Ϸ20% frequency in a natural population at Twin Cays, Belize. Here we use a battery of 36 microsatellite loci to document a striking genetic pattern (high intraspecimen heterozygosities and low within-population linkage disequilibria) that differs qualitatively from the highly homozygous (or ''clonal'') genetic architecture characteristic of killifish populations previously studied in Florida, where males are much rarer. These findings document that outcrossing (probably between gonochoristic males and hermaphrodites) is common at the Belize site, and, more importantly, they demonstrate the dramatic impact that functional androdioecy can have on the population genetic architecture of this reproductively unique vertebrate species.A ndrodioecy is a rare reproductive system in which a natural population consists of functional males and hermaphrodites but no true female gonochorists. Previously known only in a few plants (1-10) and invertebrate animals (11-15), androdioecy has also evolved independently in a vertebrate species: the mangrove killifish, Kryptolebias (formerly Rivulus) marmoratus. Most surveyed populations of K. marmoratus consist primarily or exclusively of hermaphroditic individuals, but gonochoristic males are observed occasionally, and recent genetic evidence suggests that such individuals may mediate infrequent outcross events in this otherwise self-fertilizing species (16-18). The net result, documented most clearly for Florida locales (16), is a mixed-mating population genetic architecture consisting mostly of highly homozygous inbred strains (traditionally referred to as ''clones'') plus low percentages of highly heterozygous specimens stemming from recent outcross events. Thus, the genetic variety generated by outcrossing (16), and subsequently converted into new arrays of recombinant inbred lines upon resumptions of selfing, can significantly augment mutation and interlocality gene flow that formerly were thought to be the sole sources of ''clonal'' diversity in K. marmoratus (19)(20)(21).Gonochoristic males, which are phenotypically recognizable by coloration and histology, seem to be extremely rare in Florida (in our experience, Ͻ1% frequency among Ͼ1,000 individuals examined). However, in a collection from Twin Cays, Belize, made during 1988 and 1989, 53 males (18.8%) were present among 282 specimens surveyed (22). In laboratory-reared progeny from another collection (in 1991) of hermaphrodites from this Belize locale, segregating genetic variation was detected, a result interpreted to imply that natural outcrossing had occurred between males and hermaphrodites (17, 18).In this study, we use a battery of 36 microsatellite loci to exami...