Exposed limestone karst landscapes, especially in the tropics, are often home to distinctive and specialised biotas. Amongst vertebrates, a particularly large number of karst-associated lizard taxa have been described, but for the vast majority, evidence of specific adaptions to karst is lacking. A number of studies, however, have provided evidence of consistent morphological trends in lizards that utilise complex, three-dimensional, saxicoline habitats such as those that typify karst areas. Here we combine morphological and genetic data to test whether a newly discovered gecko from an extremely rugged karst area in New Guinea shows morphological trends matching these observed in other lizards associated with complex rock habitats such as karst and caves. Consistent with predictions, the new species’ head is flatter and narrower than similar-sized relatives, and it has proportionally larger eyes and longer limbs. These trends indicate this taxon represents the second documented instance of karst specialisation in a New Guinean vertebrate, and suggest morphological traits to test for evidence of specialised ecological associations in the many karst-associated Cyrtodactylus taxa from Southeast Asia.