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Herpetofauna monitoring can be strongly limited by terrain accessibility, impeding our understanding of species ecology and thus challenging their conservation. This is particularly true for species living in the canopy, on cliffs or in dense vegetation. Remote sensing imagery may fill this gap by offering a cost-effective monitoring approach allowing to improve species detection in inaccessible areas. We investigated the applicability of drone-based monitoring for a Critically Endangered insular gecko (Phelsuma inexpectata) and two invasive alien species representing a risk for the former (P. grandisandP. laticauda). We determined the approach distance before inducing behavioural response caused by the drone’s presence. All three study species showed no reaction to the drone’s presence until very close distances (mean distance forP. inexpectata: 33.8 cm;P. grandis: 21.9 cm;P. laticauda: 26.4 cm). We then performed horizontal and vertical approaches, taking photos every meter starting at 10 m away from the canopy edge to determine an optimal distance for detection while ensuring species-level identification. We examined a total of 328 photos. We found a bimodality in the number of detected geckos, with different individuals recorded between short and intermediate distances. Therefore, we recommend taking photos at two distances of 2–2.5 m and 5 m away from the canopy, ideally facing away from the sun and in low wind conditions. We encourage the application of our methodology forPhelsumaspp., but also for other species of similar size and ecology to improve detection in inaccessible areas.