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A new population of velvet worms (Onychophora) inhabiting a lava tube cave in the island of Santa Cruz, Galapagos, is reported here. The population size is large, suggesting that they may be troglophilic. Its members are darkly pigmented, with no obvious troglomorphic features. Their 16S rRNA sequence showed no differences when compared to an unidentified species of surface velvet worm from the same island, thus supporting cave and surface populations belong to the same species. Based on the 16S rRNA data, the Galapagos velvet worms derived from an Ecuadorian/Colombian clade, as would be expected of ease of dispersal from the nearest mainland to the Galapagos Islands.