Wild relatives of domesticated Capsicum represent substantial genetic diversity and thus sources of traits of potential interest. Furthermore, the hybridization compatibility between members of Capsicum species complexes remains unresolved. Improving our understanding of the relationship between Capsicum species relatedness and their ability to form hybrids is a highly pertinent issue. Through the development of novel interspecific hybrids in this study, we demonstrate interspecies compatibility is not necessarily reflected in relatedness according to established Capsicum genepool complexes. Based on a phylogeny constructed by genotyping using simple sequence repeat (SSR) markers and with a portion of the waxy locus, and through principal component analysis (PCA) of phenotypic data, we clarify the relationships among wild and domesticated Capsicum species. Together, the phylogeny and hybridization studies provide evidence for the misidentification of a number of species from the World Vegetable Center genebank included in this study. The World Vegetable Center holds the largest collection of Capsicum genetic material globally, therefore this may reflect a wider issue in the misidentification of Capsicum wild relatives. The findings presented here provide insight into an apparent disconnect between compatibility and relatedness in the Capsicum genus, which will be valuable in identifying candidates for future breeding programs.