How genetic variation influences phenotypic variation is of importance to many biological disciplines, including evolutionary biology, biomedicine, and agriculture. Nevertheless, students frequently struggle to make connections across levels of biological organization, which can make it challenging to facilitate understanding of how nucleotide variation gives rise to organismal variation. At the same time, biology students are now expected to gain early experience with cornerstone techniques from molecular biology, so that these skills can be reinforced and expanded upon. Here we describe a five-to-seven-week sequencing project that examines genetic and phenotypic variation in wild-type and yellow-bodied fruit flies and, in the process, exposes students to several foundational techniques in molecular biology. In addition, students analyze partial yellow gene sequences from PCR products using the freely available bioinformatics suite UGENE and in doing so are introduced to core bioinformatics skills. The entire project is framed around the axiom that if the yellow gene controls phenotypic differences in body color between wild-type and yellow-bodied flies, it should be possible to identify causal variation in yellow sequences from wild-type versus yellow-bodied flies. This project relies on guided inquiry and can be used in 1000- or 2000-level molecular biology courses and advanced high school laboratories.