The identification and classification of similar cryptic species such as Kryptolebias marmoratusand Kryptolebias ocellatus,as distinct species has always been problematic within the biological sciences. Though Kryptolebias marmoratusand Kryptolebias ocellatusare both known to be self-fertilizing hermaphrodites, out crossing has been observed resulting in heterozygous offspring. Recently, a viable hybrid (Gitmo) between K. marmoratusand K. ocellatushas been isolated in the Valdosta State University aquatic lab. This hybrid questions the proposed species status of these fishes. Classifications of organisms are usually based on both morphological and genotypic studies. Based on morphological studies, both fishes were thought to be synonymous because of very similar anatomical and physiological characteristics. Mitochondrial studies (genotypic analysis) ofthese fishes have suggested otherwise. Unfortunately, thorough whole genome studies are very expensive and labour intensive. Methods such as Restriction Fragment Length Polymorphisms (RFLP), Amplified Fragment Length Polymorphisms (AFLP) and microsatellite analysis are more commonly used. These methods, though helpful, make analyses based on the length polymorphisms of the DNA fragments and only a small portion of the genome. Furthermore, surveys yield a very limited amount of genetic information. A more reliable method of analyzing large numbers of these genotypic markers concurrently would be extremely valuable for taxonomic questions. Developing Restriction Associated DNA Tag (RADTag) genome sequencing using methods for the Ion Torrent Personal Genome Machine (PGM) provides a way not only to cut down the cost of genomic sequencing but also provides a method that performs thousands of Single Nucleotide Polymorphisms (SNP) analyses atonce, without the use of a reference sequence. Analysis of RADTag sequences on public domains “Stacks” software displayed thousands of markers present in the Hon9 (Kryptolebias marmoratus) genome and confirms the Hon9 strain to be highly homozygous (0.999) across all loci. This achievement paves the way for further genomic studies with high throughputs and accuracy. This RADtag genome will provide the information needed for resolving the questionable relationship between K. marmoratusand the presumptive K. ocellatus cryptic species.