Tomato and pepper landraces and cultivars exhibit diverse fruit morphology, contributing to many different uses and market niches. The genetic underpinnings of that diversity are interesting from both applied and basic developmental research perspectives. This dissertation catalogues genetic diversity in a set of pepper and tomato landrace and wild-growing accessions, with a focus on how such genetic diversity underlies fruit shape diversity. Genotyping-by-sequencing, structural variant analysis, QTL-mapping, and coexpression network analysis are all employed to explore that diversity. These analyses result in a genetic description of the population structure of pepper landraces from southern Mexico, a refined understanding of the position, gene action, and phenotype of the pepper fruit-shape QTL fs3.1, coexpression networks of several tomato TRMs which putatively underlie fruit shape, and a set of structural variants intersecting genes in said coexpression networks. These point to a shared mechanism controlling fruit shape in pepper and tomato, and provide resources for further study of fruit shape in both.