Tomato is one of the major vegetable crops. The wild relatives of cultivated tomato are a source of agronomically important germplasm but sexual crosses between them and the cultivated tomato are limited due to unilateral and bilateral incompatibility barriers. The aim of this review is to outline nuclear—cytoplasmic interrelations on the basis of interspecific and somatic hybridization data with the species from genus Lycopersicon. An attempt is done to summarize the published results of the studies on the mitochondrial genome of species, interspecies and somatic hybrids as well as the results concerning cytoplasmic male sterility in the genus Lycopersicon.