The Humboldt Archipelago, situated on Chile’s north-central coast, is renowned for its exceptional biodiversity. However, lizards of the Liolaemus genus are a particularly understudied group in this archipelago. Liolaemus genus is divided into two clades: chiliensis and nigromaculatus. Within the nigromaculatus clade the zapallarensis group is restricted to the semi-arid and arid coastal habitats of the Atacama Desert in north-central Chile. While it has been reported that lizards from the zapallarensis group inhabit various islands within the Humboldt Archipelago, there has been limited knowledge regarding their specific species identification. To identify the lizard species inhabiting these islands, we conducted phylogenetic analyses using a mitochondrial gene and examined morphological characteristics. Our findings reveal that lizards from the Damas, Choros, and Gaviota islands belong to Liolaemus silvai. In contrast, the lizards on Chañaral Island form a distinct and previously unrecognised group, clearly distinguishable from Liolaemus silvai. In conclusion, our study not only confirms the presence of L. silvai on the Damas, Choros, and Gaviota islands but also describes a new lizard species on Chañaral Island named Liolaemus carezzae sp. nov. These findings contribute valuable insights into the biodiversity of these islands and introduce a newly discovered endemic taxon to the region, enriching our understanding of Chile’s unique island ecosystems.