A pygmephorid mite, Luciaphorus perniciosus Rack, is widely spread in several commercial mushroom production settings in Thailand. This mushroom mite was collected from Lentinus squarrosulus (Mont.) Singer compost and basidiocarps from several farms located in 4 different provinces (Maha Sarakham, Kalasin, Roi Et and Ubon Ratchathani) of the Northeast of Thailand. The other specimens were provided by the Department of Agriculture, Thailand, which were previously collected from Ubon Ratchathani province. These mite samples could not be differentiated into sub-groups by external morphological examination, even though they appeared to have some minor morphological characteristics different from the prototype L. perniciosus. The RAPD-PCR profile and genetic distance information of the 5 populations could categorise these mites into 3 groups; mites in Group 1 which were collected from Maha Sarakham; Group 2 from Roi Et and Ubon Ratchathani-Bangkok and Group 3 from Kalasin, Ubon Ratchathani, Roi Et and Ubon Ratchathani-Bangkok. The results thus indicate that although all mites in this study were L. perniciosus, they are genetically diverse. © 2011 Academic Journals.