Reciprocal crosses involving Solanum gilo Raddi, S. anguivi Lam. and S. macrocarpon L., subg. Leptostemonum (Dunal) Bitter sect. Melongena Dunal were produced in order to assess inherent nuclear and non-nuclear influences on hybrid fitness, the extent of genomic change, and species compatibility. Hybrids expressed intermediacy and overlaps in leaf, petiole, petal, and plant height dimensions. Maternal influence was dominant in growth habit, leaf shape and texture, flower colour, and fruit size, while paternal control was limited to fruit colour in Solanum gilo × S. macrocarpon. Pollen viability was reduced from 97.3%-86.5% in parents to 53.8%-20.5% in hybrids. S. gilo × S. macrocarpon produced single-flowered inflorescence, whereas the reciprocal S. macrocarpon × S. gilo developed the ability to perennate, indicating the heterogeneity of the parental genome. Fruits of the hybrids were intermediate or smaller, and had fewer seeds. They were wrinkled in S. gilo × S. macrocarpon, with many aborted seeds. Meiosis was irregular, with few laggards, and isolated uni- and bivalent chromosomes associated with foreign genes in the parent species. Conversely, multivalent and chromosome clumps revealed the extent of homogenization of the parental genomes and species affinity. The maternal genome exerted profound influence on hybrid phenotype and fitness, and should inform and direct future hybridization efforts.