The genus Basidiobolus contains large groups of terrestrial fungi including the etiological agents of human gastrointestinal basidiobolomycosis (GIB). This study aimed to identify Basidiobolus species from the common house gecko and to compare them with human GIB isolates. Gecko and human GIB samples were collected from Muhayil Aseer area, south Saudi Arabia (2017-2019). Isolation of fungi from the gut contents of geckos was performed using Sabouraud dextrose agar incubated aerobically at 30°C for five days. Suspected Basidiobolus species were tentatively identified using routine bench tests and phenotypes were authenticated by phylogenetic analysis of the large subunit ribosomal RNA gene. Isolates (n = 10) were found to have zygomycete-like phenotypic characteristics. In the 28S ribosomal RNA gene phylogenetic tree, the strains assembled in the subclade encompass Basidiobolus spp. along with previously reported isolates from human' GIB. The strains had a close resemblance with Basidiobolus haptosporus (99.97%) as well as with B. haptosporus var. minor (99.97%). One isolate (L3) falls within the subclade containing B. haptosporus strain NRRL28635. The recovery of similar isolates from both humans and gecko lizards in one geographic region is an important development toward knowing risk factors for GIB.