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Aim To understand the patterns of genetic, geographical and morphological diversification in the Arabian gecko subspecies Pristurus rupestris rupestris, and to discuss the various processes that generate and shape diversity in arid mountain ranges.

Location Hajar Mountains, south-eastern Arabian Peninsula.

Methods We sampled 466 individuals across the entire range of P. r. rupestris in the Hajar Mountains and sequenced one mitochondrial gene for all the samples, and one extra mitochondrial and four nuclear genes for a subset of 75 specimens. A total of 155 individuals were characterized morphologically. Multilocus coalescent-based methods were used for species delimitation, for phylogenetic inference of species trees and to investigate the diversification dynamics. Multivariate statistics were used to analyse morphological data.

Results Our molecular methods revealed 14 candidate species hidden within the subspecies P. r. rupestris. Diversification started c.15Ma, but most of the lineages have evolved in the last 7Ma of the mountains’ orogeny, producing a mosaic of allopatric taxa. Secondary interchange has occurred between high and low elevation lineages, and along the mountain chain between unrelated lineages formerly separated by mountain blocks. Morphological variation between the 14 candidate species is slight, but a high elevation robust morphotype is identified.

Main conclusions Our results support the notion that mountain ranges constitute important centres of diversification in arid regions, and also act as species pumps’ into surrounding areas. We also demonstrate that arid mountains may constitute important reservoirs of cryptic diversity, even in common and widespread species. This, and previous evidence, suggest that the Hajar Mountains are a biological hotspot and an important reservoir of diversity. We therefore suggest that these mountains should be a priority focal point for conservation in Arabia.