Species with disjunct geographic distributions provide natural opportunities to investigate recent or incipient allopatric divergence. Although not rare, many of the cases observed result from successful colonization from a historical to a new range through dispersal or human-induced introduction which make the underlying eco-evolutionary processes sometimes difficult to decipher. The Ophrys aveyronensis species complex presents a disjunct geographic distribution with two ranges currently separated by 600 km on both sides of the Pyrenees Mountains. To uncover the causes of such intriguing biogeographic pattern, we combined population genomics and Ecological Niche Modelling approaches. Population genomic data show that all the populations studied display similar patterns of genetic diversity and dramatic decrease in effective size. We found significant genetic differentiation between the two ranges of the O. aveyronensis species complex. Our results indicate a recent divergence (i.e. about 3500 generations ago). Ecological Niche Modelling results further support that the disjunct geographic distribution of the O. aveyronensis species complex is consistent with a range split of a broad ancestral range, contraction and shifts in opposite directions in response to climate warming since the Last Glacial Maximum (LGM, about 21000 years ago). The congruence of both the results of population genomics and ENM approaches indicate that allopatric speciation is involved in the Ophrys adaptive radiation. The O. aveyronensis complex thus provides a promising candidate to further investigate putative incipient ecological divergence following an initial phase of geographic isolation.