A survey of digenean zoonotic trematodes infecting snails and fishes in a North Vietnamese freshwater fish culture system revealed shedding of three types of parapleurolophocercous cercariae from the snail host Melanoides tuberculata and the presence of metacercariae within the genus Haplorchis (H. pumilio and H. taichui) and Procerovum sp. in tissues of cultured fishes (silver carp, Indian carp and climbing perch). No morphological characters were able to link the different cercariae specifically to any of the metacercariae. Subsequent molecular work including PCR and sequencing of ribosomal DNA (the ITS2 region) in cercariae and metacercariae associated only one type of the cercariae to the recovered H. pumilio metacercariae. Further, full identity (100%) was found with regard to the ITS sequence of adult H. pumilio obtained from the same North Vietnamese region. None of the cercariae showed sequence identities with H. taichui but more than 99% identity was found between one cercaria type and the Procerovum sp. metacercaria. It was indicated that trematode parasites of farmed fishes may originate from sources outside the fish ponds and may be introduced as free-swimming cercariae when pond water is being replenished by river water. Likewise, cercariae from the ponds may not always result in metacercarial infections of the farmed fishes. The present study frames the needs for including molecular techniques as auxiliary tools when conducting ecological studies of cercariae in complex ecosystems. The parasites recorded in the fish ponds are not only known to affect the health of aquacultured fishes but also the documented zoonotic potential of the diagnosed metacercaria calls for alerts regarding human consumption of raw or inadequately processed fish dishes.