To better understand the population dynamics of the pathogens at disease nursery and field, we studied the pathogens population at two disease nurseries located in Shanghang and Jiangle counties and their nearby fields with virulence analysis based on CO39 near isogenic lines (CO39 NILs) and DNA fingerprint patterns defined by a repetitive element (Pot-2) based polymerase chain reaction (rep-PCR). The prevalent lineage was CFL03 in 1999 and 2000, and was CFL07 in 2001. The prevalent lineage was CFL07 in early and late season in the nursery and field in Jiangle County. The prevalent pathotype was I20.1 in 1999 and were I4.1 and I14.1 in 2000. The prevalent pathotype was I14.1 in early season and was I20.1 in late season in 2001. The use of traditional and molecular techniques will improve the efficiency of screening new varieties for resistance. It will also be beneficial to deepen the understanding of the relationship between the pathotype and genetic lineage, and to breed for durable resistance in rice varieties.