Epidermal appendages are found on every vertebrate this world has to offer. In fish, these are commonly represented by scales. While we have a solid grasp of how scales develop, little is known about the underlying genetic mechanisms behind these phenotypic changes. Using two species of African cichlids (Labeotropheus fuelleborni and Tropheops “red cheek”) with varying scale phenotypes, we sought to examine their F2 hybrid offspring and statistically link the responsible genetic elements to their respective parental phenotypes through Quantitative Loci Trait (QTL) analysis. Scales were removed from six different locations across the midline of each individual. Then, numerous traits on each scale were measured, and these values were used in the QTL analysis. 42 significant QTL were identified, with multiple QTL intervals possessing promising candidate genes. These genes include: fgfr1b, efna5a, TGIF1, eIF6, and col1a1a. Previous studies have implicated these particular genes and gene families to play important roles in scale and placode development. However, they represent the minority of QTL intervals discovered, providing direction for future research towards the other QTL intervals represented by this study.