Infection by Penicillium marneffei in human immunodeficiency virus-positive patients in India has recently been described; the aim of our study was to survey wild rodents and their associated environment in order to identify the natural populations of this fungus. Surveys recovered P. marneffei from the internal organs of 10 (9.1%) of 110 bamboo rats (Cannomys badius) examined from Manipur state, India, an area endemic for penicilliosis marneffei. Identification of the isolates was based on a detailed study of their morphological characteristics, in vitro conversion to fission yeast form, and exoantigen tests. Multilocus microsatellite typing (MLMT) of the isolates revealed five genotypes. No genotypes were shared between sample sites, and all bamboo rats were infected with a single genotype within sample sites, demonstrating spatial genetic heterogeneity. One MLMT genotype was identical to that seen in a human isolate, suggesting that either coinfection from a common source or host-to-host transmission had occurred. This demonstrates the utility of an MLMT-based approach to elucidating the epidemiology of P. marneffei.Penicillium marneffei is the only dimorphic species of the genus Penicillium and is the etiological agent of penicilliosis marneffei. This opportunistic fungal infection occurs among human immunodeficiency virus (HIV)-infected and other immunocompromised patients in several regions of southeast Asia. Areas where P. marneffei infection is known to be endemic include Thailand, southern China, Taiwan, Hong Kong, Malaysia, Indonesia, Viet Nam, Myanmar (Burma), and Manipur state in India (10,11,23,27,28). A single case of the disease in an African from Ghana, who had no history of travel to Asia, has also been described (21). Several cases of penicilliosis marneffei have been reported from Europe, the United States, Australia, and Singapore in patients who had prior history of visits to areas where the infection is endemic (17,28).Initial isolation of P. marneffei was from a captive bamboo rat (Rhizomys sinensis) used for laboratory experiments in South Vietnam (3). The native bamboo rat had been experimentally inoculated with the scrub typhus bacterium Rickettsia orientalis (now designated Rickettsia tsutsugamushi). At autopsy, the rodent was found to have an enlarged liver and spleen, viscous ascitic fluid, and epiploic nodules. Cultures from all the organs yielded a Penicillium species, which proved pathogenic to hamsters (Mesocricetus auratus). The fungus was subsequently described as a new species by Segretain (25), who named the fungus Penicillium marneffei in honor of Hubert Marneffei, then-director of the Pasteur Institute in French Indochina. In later decades, several workers investigated the prevalence of P. marneffei in bamboo rats in different geographic areas (1,5,9,20,29,33). Four species of bamboo rats, R. sinensis, Rhizomys pruinosus, Rhizomys sumatrensis, and Cannomys badius, were identified as natural hosts of P. marneffei (1, 5, 9). The aim of the present study was to investigate whe...