Phylogenetic discordance among taxa can provide powerful insights into past episodes of introgressive hybridization, as well as lineage sorting. Previously, we showed that the taxonomically distinct taxon Rhinolophus sinicus septentrionalis has undergone historical introgression with its sympatric sister subspecies Rhinolophus sinicus sinicus. To examine in more detail the extent of gene flow between these two taxa, and also between these and their sister species Rhinolophus thomasi, we obtained new samples from China, Myanmar, and Vietnam, and combined new and published genetic data from these, Rhinolophus rouxii, and Rhinolophus indorouxii from India. Phylogenetic analyses revealed three separate cases of discordance: between R. s. septentrionalis and adjacent populations of R. s. sinicus, between R. s. septentrionalis and R. thomasi and between eastern populations of R. s. sinicus and a newly-identified lineage. In both former cases, the mitochondrial DNA introgression appears to be asymmetric, which is likely to have resulted from mating between R. s. septentrionalis females with smaller R. s. sinicus and R. thomasi males, although we cannot rule out other scenarios completely. Further conflicts between genetic data and accepted species arrangements across the genus, with paraphyly of members of the rouxii-group, suggest the need for a thorough systematic revision of relationships within this group.