The infection dynamics of metacercariae were assessed in cyprinoid fish (cyprinoids) from Chiang Mai and Sakon Nakhon Provinces, Thailand, during October 2008 to September 2009. The samples were collected during 3 seasons from rivers and local markets. Metacercarial infection was determined by acid-pepsin digestion and confirmed using HAT-RAPD PCR method. Thirteen and 16 species of cyprinoids were collected from Chiang Mai and Sakon Nakhon with overall prevalences of metacercarial infection of 84.5 and 47.6%, respectively. Haplorchis taichui, Haplorchoides sp, and Centrocestus caninus were found in Chiang Mai and 4 species of metacercariae: H. taichui, Haplorchoides sp, O. viverrini and an unknown trematode species in Sakon Nakhon. H. taichui and Haplorchoides sp metacercariae in 3 species of cyprinoids (Henicorhynchus siamensis, Cyclocheilichthys armatus, Amblyrhynchichthy truncatus) had the highest prevalence (100%) in Chiang Mai, while the highest prevalence (100%) of metacercaria in Sakon Nakhon was Haplorchoides sp in 1 species of cyprinoids (Cyclocheilichthys armatus). The overall prevalence from Chiang Mai Province was highest in the rainy season (95.6%), lower in the hot-dry season (88.1%) and lowest in the cool season (72.5%). In Sakon Nakhon Province the highest prevalence was in the hot-dry season (52.7%), and lower in the rainy and cool season, 44.4% and 43.5%, respectively. The HAT-RAPD profiles confirmed the identity of metacercariae and adult stage of H. taichui, Haplorchoides sp, C. caninus and O. viverrini.