Pleistocene climate cycles have been recognized to be a major driver of postglacial northward range expansion of North American bird populations. During glacial maxima, allopatric lineages that were reproductively isolated might have come into secondary contact with one another during expansion periods and the genetic signatures of past hybridization as a result of secondary contact events should produce detectable hybrid zones. The white-chested hummingbirds, Amazilia violiceps and A. viridifrons, constitute a species complex showing phenotypic similarity across its range. One exception is the subspecies found in the Central Depression of Chiapas (A. viridifrons villadai), which shares some plumage traits with the endemic but allopatric green-fronted populations in Oaxaca. Phylogenetic relationships, taxonomy and species limits among violiceps, viridifrons and villadai have been controversial for decades. We assessed genetic structure of populations and introgression in this species complex by analysing 95 individuals at ten nuclear microsatellites and morphology. Bayesian analysis yielded four clusters. However, only two clusters generally match previously described mtDNA haplogroups, one parental taxon in the south (villadai) and a cluster with two admixed taxa (viridifrons and violiceps) that cannot be attributed to any pure parental population. High genetic admixture was recorded in the violiceps/viridifrons range, probably as a consequence of a postglacial northern expansion of violiceps. Signs of admixture and gene flow between violiceps/viridifrons and villadai were low. Historical and contemporary migration rates and Approximate Bayesian computations support a scenario of divergence with gene flow: a Pleistocene basal split separating A. violiceps and the other two clades are derived from a second split (villadai and viridifrons) or from a merger of violiceps and villadai into viridifrons due to gene flow.