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 geryi and Varanus exanthematicus. All taxa included, as well as other related taxa not included in our study, are exploited heavily by the international skin and pet trades, yet researchers and conservation agencies currently lack substantial genetic resources for guiding conservation and management. Using stringent filtering methods, we generated between 467 and 8641 PALs for each of the ten species (52,164 PALs total), yielding a rich database of microsatellite loci and amplification primers for these taxa. In addition to the ten species targeted in our study, microsatellite markers provided in this database can likely be applied to a variety of closely related taxa that are also of conservation and commercial interest. ; PALsPAL files are provided for each species described in the publication in text format.A_gran_readsA_pras_readsC_rhyn_readsG_kuhl_readsT_grac_readsT_saba_readsU_geyr_readsV_exan_reads