The Artibeus jamaicensis complex is an important component of the mammal biological diversity of the New World. Although there are numerous studies on the taxonomy and phylogeny of the complex, group relationships are still debated. Previous studies hypothesised that this species originated in South America and later colonised the Antilles Islands either through a northward migration or an eastward migration via Middle America. However, these studies do not include populations from Middle America west of the Yucatan Peninsula, making it difficult to obtain a clear description of the role of these populations in the evolutionary history of the species. In this study, we describe the phylogeography and demographic history of A. jamaicensis populations from Middle America west of the Yucatan Peninsula using cytochrome-b (612 bp) and D-loop (391 bp) mtDNA markers. Our phylogenetic analyses (maximum likelihood and Bayesian inference) did not recover clades corresponding to the previously recognised Middle American subspecies (A. j. triomylus and A. j. yucatanicus); rather, two haplogroups were observed, which showed extensive genetic diversity and strong genetic structure akin to that expected for a Middle American origin for the island populations. Bayesian skyline plots and mismatch distributions revealed that such haplogroups experienced a recent population expansion, which most likely took place in the late Pleistocene (100,000–216,000 BP). These estimates agree with earlier hypotheses that suggested a recent evolutionary history for A. jamaicensis, with hypotheses that suggested the existence of two different lineages migrating northwest from South America to Middle America, and with the possible colonisation of the Antilles Islands derived from both Yucatan Peninsula and northern South America.