Abstract: Despite extensive theory existing on the roles natural selection can play in speciation, the uniqueness of lineages and environmental contexts often makes partitioning the drivers of diversification difficult in practice. Specifically, disentangling the relative contributions of spatial isolation and natural selection in initiating speciation remains a challenge. One way to infer the role of natural selection in evolution is by examining parallel patterns of diversification within a species complex. Because the Midas cichlid fishes (Amphilophus sp.) in Nicaragua colonized multiple crater lakes independently and diversify along various ecological axes, they are an excellent system for studying natural selection and are the focus of the research I will present. First, I will demonstrate that there is parallel eco-morphological evolution of these fish species and a parallel pattern of evolutionary branching in sympatry across crater lakes. Second, I will describe how signals of positive selection from whole transcriptome sequence analyses suggest non-parallel genetic bases to this eco-morphological evolution. Third, I will discuss the relevance of other axes of phenotypic differentiation to the evolution of this species complex. Together this shows how a combined genomic and phenotypic approach on populations in nature can partition natural selection from geographical isolation in speciation.