The incidence of Penicillium marneffei infection has increased substantially, especially in persons with HIV infection. Very little is known about the natural reservoirs or animal hosts of P. marneffei. This pathogenic fungus was first isolated from a species of bamboo rat (Rhizomys sinensis) in Vietnam and later from another rodent species, R. pruinosus. We studied a total of 75 captured bamboo rats; P. marneffei could be isolated from the internal organs of 13 of 14 (92.8%) of large bamboo rats, R. sumatrensis, and of 3 of 10 reddish-brown small bay bamboo rats, Cannomys badius (30%). All 51 greyish-black C. badius were negative on culture. Among R. sumatrensis, P. marneffei were frequently recovered from the lungs (85.7%), spleen (50%) and liver (28.6%). Of the 28 soil samples collected from the bamboo rat burrows and the 67 from the residential areas of patients with P. marneffei infection, P. marneffei was isolated from one soil sample collected from a burrow of R. sumatrensis. The mycological characteristics of P. marneffei isolates from bamboo rats and humans were very similar. Our data indicate that R. sumatrensis and C. badius may be important animal hosts of P. marneffei in northern Thailand.