Here we document the addition of thousands of potentially amplifiable microsatellite loci (PALs) and associated primer sequences for public use. We conducted whole-genome shotgun sequencing to obtain ultra-low coverage, random genomic sampling from ten African and Asian squamate reptile species (representing ten genera). We used unique genomic processing methods and generated PALs for the following species: Acrochordus granulatus, Ahaetulla prasina, Cerberus rhynchops, Gonocephalus kuhlii, Ophiophagus hannah, Python bivittatus, Tribolonotus gracilis, Trimeresurus sabahi (Popeia sabahi), Uromastyx...