Malus toringoides Hughes and its close relatives, M. maerkangensis M. H. Cheng et al., M. setok Vassilcz., and M. xiaojinensis M. H. Cheng & N. G. Jiang were supposed to derive from hybridizations. However, molecular data are still inadequate to corroborate the hybrid origin hypotheses. In this study, we sequenced a single-copy nuclear gene SbeI and three chloroplast fragments and carried out phylogenetic analyses to investigate the evolutionary origins of the above four putative hybrid taxa. The hybrid nature of M. toringoides is confirmed by the detection of two distinct types of SbeI sequences from it. The chloroplast and SbeI gene phylogenies show that the maternal progenitor of M. toringoides is closely related to M. sikkimensis N. P. Balakr. and M. spectabilis Borkh., and the paternal progenitor is most likely M. transitoria C. K. Schneid. The hypothesis that M. kansuensis (Batalin) C. K. Schneid. is one of the parents of M. toringoides is not supported. Malus maerkangensis and M. xiaojinensis might have originated through hybridization between M. toringoides and M. kansuensis, whereas M. setok is genetically closely related to M. toringoides. The three close relatives of M. toringoides were designated as three novel species by some researchers, however, as they were all apomictic with limited distribution areas and they originated from hybridization and polyploidization, we recommend that their species status should be re-evaluated.