AbstractHere we study a challenging group of karyotypically highly variable Epidendrum spp. using phylogenetic methods to help understand how hybridization/introgression contributes to karyotype evolution. We hypothesize that species with great chromosome number variation are a result of past hybridization/introgression. Conflicting topologies in trees constructed using separate plastid and nuclear datasets suggest past hybridization events that occurred most probably at least 3.7 Mya. A basic number x = 14 and substantial karyotype change followed by species divergence are suggested. Descending dysploidy and polyploidy were the most frequent changes estimated across the phylogenetic tree of the group. Two species, Epidendrum secundum and E. xanthinum, have probably experienced unidirectional gene flow involving their ancestors (the pollen recipients) and ancestors of E. puniceoluteum and E. denticulatum/E. flammeum, respectively, the pollen donors. However, it is not possible to say whether hybridization participated in the origin of E. secundum and E. xanthinum or merely contributed to their genomic divergence and karyotype change through introgression as has been observed in modern hybrid zones in Epidendrum. This pattern of introgression causing karyotype disruption and divergence could help explain the enigma of some highly diverse genera, such as Epidendrum. Further studies using a wider sampling of the genus could test if gene flow and karyotype variability are associated with the increase of speciation rates.