The cichlids of East Africa are a well-known group of fishes that display a wide range of phenotypic diversity, including differences in tooth shape, facial and body morphology, visual palettes, and body coloration. This diversity in phenotype was generated within the last 10 million years via an adaptive radiation. The cichlids of Lake Malawi are particularly known for their wide variation in male color patterns, which is thought to have been driven by sexual selection. Given their recent evolution, different species of cichlids can be intercrossed in the lab to identify the underlying genetic basis of phenotypic traits via a forward genetics approach. Using this methodology, I created a hybrid cross between two cichlid species, Metriaclima zebra and M. mbenjii that differ in several pigmentation traits in an attempt to identify the underlying genetic basis of these traits. After quantifying these pigmentation traits, I was able to use the Castle-Wright equation to estimate that a small number of genes underlie these traits. I was then able to identify quantitative trait loci (QTL) for three traits, dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. The QTL for dorsal and caudal fin xanthophores were found to overlap on the same linkage group. I was able to identify and preliminarily analyze the candidate gene, AAK1, for this shared QTL region. In addition to this pigmentation work, I was also able to identify a genomic region where a potential XY sex determiner is located and analyze a candidate gene, GSDF.