An aquatic animal's microbiome, is vital to its nutrition, growth, and overall health. Exogenous factors such as diet and the rearing environment are known to affect the microbiome. However, little is known about the role that host genetics plays on the microbiome structure. To investigate the potential influence of host genetics on the community of microorganisms present in the host, skin and intestinal epithelial tissues were harvested from three proprietary family lines of Nile tilapia (Oreochromis niloticus) that differ by one genetic trait. Prior work demonstrated that one of the genetically-related lines has a much higher growth rate than the other two, when age and environmental conditions are controlled. It was hypothesized that the animal's microbiome was a contributing factor to the observed differences in growth. Therefore, the V4 region of the bacterial 16S rRNA gene was amplified using DNA separately extracted from the scales or midgut portions of the intestines. The resulting PCR products were gel purified and sequenced via Illumina Mi-Seq protocols. Preliminary QIIME bioinformatics analysis of the intestinal samples has revealed noticeable differences in the microbiome structure between the faster growing fish and the other family lines. The most abundant bacterial families in the more productive fish line, Mycoplasmataceae and Fusobacteriaceae, are virtually absent in the other two lines, which have higher levels of Enterobacteriaceae. Analysis of scale samples is on-going. Thus, fish lines differentiated only by the alteration of a single trait exhibited differences in the host-associated microbial communities.