The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of cryptic diversity and revealed numerous taxonomic complications, especially within the C. consobrinus, C. malayanus, and C. pubisulcus groups. Comparisons of pairwise genetic distances and a preliminary species delimitation analysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-ranging species on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricted distributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneo into the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derived from multiple separate invasions into the geopolitical areas comprising the Philippines. Although our investigation of Bornean Cyrtodactylus is the most comprehensive to-date, it highlights the need for expanded taxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeography of Bornean Cyrtodactylus is far from complete.

The island of Borneo lies within one of the most biodiverse regions in the world. Despite this, its documented gekkonid diversity is not commensurate with other areas of Southeast Asia. The megadiverse genus Cyrtodactylus is especially underrepresented. Limestone-karst ecosystems, in particular, harbor many endemic Cyrtodactylus species, but only one karst-dwelling species is currently recognized from Borneo. This paper adds two additional karst-dwelling Cyrtodactylus species—C. muluensis sp. nov. and C. limajalur sp. nov.—from Sarawak, Malaysia. Cyrtodactylus muluensis sp. nov. is endemic to Gunung Mulu and is distinguished from its congeners by having a precloacal groove, 31–38 ventral scales, a maximum SVL of at least 88 mm, enlarged subcaudals, 19–20 subdigital lamellae, and a banded dorsal body pattern. Cyrtodactylus limajalur sp. nov. is endemic to the Serian region and is distinguished from its congeners by having 33–42 ventral scales, enlarged subcaudals, a precloacal pit, a maximum SVL of at least 94 mm, 5–6 enlarged femoral scales, 19–22 subdigital lamellae, and five distinct bands on the dorsum. Both species are phylogenetically distinct and deeply divergent from all other congeners. The description of two new karst-dwelling species highlights the need to conserve karst habitats and the endemic species they harbor.

The appreciation of cryptic biological diversity, and the pace at which it is recognized, has greatly increased with the use of molecular systematic techniques. The gekkonid genus Cyrtodactylus Gray, 1827 is one example of a group that has undergone a particularly rapid increase in recognized diversity due to molecular systematic studies. Many of these new species result from recognizing closely related but diagnosable lineages into sister taxa. Our study implements a multi‐faceted approach to delimit cryptic Cyrtodactylus lineages on the Southeast Asian island of Borneo using morphological, ecological, and multilocus genetic data. We use multiple species delimitation models to assess species boundaries and identify clades that warrant further investigation. Unlike most morphologically cryptic species that have recently diverged, we find evidence of cryptic lineages being polyphyletic. Using multivariate statistical analyses, we show minimal phenotypic distinction between putative cryptic species within the C. pubisulcus complex. Despite not finding morphologically diagnostic characters, we demonstrate strong evidence for the specific recognition of C. hantu sp. nov. and C. miriensis sp. nov., which are currently considered conspecific with C. pubisulcus, from Sarawak, Malaysia. Our new concept for C. pubisulcus restricts the geographic range of the species to specific regions in western Sarawak, Malaysia, thus underscoring the need to conserve the limited remaining habitats of these species, as well as the considerable undescribed diversity across Borneo.

Three new species of Cnemaspis are described from karst regions of Sarawak, Malaysia, on the island of Borneo. These are Cnemaspis matahari sp. nov. and C. sirehensis sp. nov. from limestone hills located in the Serian Division of western Sarawak, and C. lagang sp. nov. from Gunung Mulu, Miri Division, in northern Sarawak. All can be distinguished from congeners using mitochondrial DNA as well as an enlarged metatarsal scales on the first toe. Individually, each species can be diagnosed by differences in subcaudal scale morphology: Cnemaspis lagang sp. nov. lacks enlarged subcaudals; Cnemaspis matahari sp. nov. has keeled subcaudals bearing an enlarged median row of smooth scales; and Cnemaspis sirehensis sp. nov. has an enlarged median row of weakly keeled scales. The discovery of these species suggests that additional unrecognized species may exist within the genus on Borneo, especially in association with karst formations. High endemism and species diversity notwithstanding, these karst formations are under severe pressure from limestone extraction and deforestation.

Using molecular genetic data, recognised diversity within the gecko genus Cyrtodactylus has more than doubled, with many lineages that were once thought to be wide-ranging being delimited into multiple independent species. On the Southeast Asian island of Borneo, there has been a recent renewed focus on reptile taxonomy, as genetic data have demonstrated a high amount of unrecognised biodiversity. We herein advance this taxonomic trend by delimiting three distinct species within the Cyrtodactylus consobrinus species complex: C. consobrinus, C. kapitensis sp. n., and C. hutan sp. n. To do so, we use a combination of ddRADseq and single-locus data, and morphological data. Using genomic data, we test species and population boundaries within the consobrinus species complex and show minimal population structure but high species-level diversity. Despite not finding uniquely diagnostic morphological characters to delimit the new species, we suggest a combination of characters that can be used to identify each lineage.Lastly, we use our data to comment on the status of C. malayanus, with indications that this lineage is also better considered a species complex. These data highlight the prevalence of unrecognised lineages on Borneo, many of which face threats due to increasing deforestation and other anthropogenic pressures.