Squamate remains from fossil-bearing deposits are difficult to identify on the basis of their morphology, because their modern relatives lack osteological description. In addition, intraspecific morphological variability of modern taxa is mostly understudied, making taxonomic identification of subfossil bones even more difficult. The aim of this study was to investigate osteological differences between two sympatric gecko species, Thecadactylus rapicauda and Hemidactylus mabouia, both currently occurring in the Lesser Antilles and in the subfossil assemblages of the region. Comparison of several modern museum specimens reveals the intraspecific osteological variability of these lizards and how difficult it is to distinguish between their bones, even though they are from two distant families. This study presents nine osteological characters, allowing for a fully reliable distinction of these two gecko species. These characters are applied to the specific identification of gecko species subfossil remains unearthed from the Pointe Gros Rempart 6 Hole (La Désirade Island, Guadeloupe). Our results confirm the past occurrence of T. rapicauda as well as the historical introduction of H. mabouia on La Désirade Island.