Background: Hydroids were identified from extensive surveys of benthos, and especially from worm tubes, in the Danshuei River estuary (DRE), in the northeast Taiwan Strait (NETS), and on a reef in Nanwan Bay (NWB), Taiwan. Results: A total of 33 species (12 of them identified to generic and 1 to family rank only), referable to 22 genera, 12 families, and 2 orders, were distinguished. The majority of them were referable to order Leptothecata (84.8%) with the remainder being assigned to order Anthoathecata (15.2%). The only species found at NETS was Monoserius pennarius (Linnaeus, 1758). Plumularia habereri (Stechow, 1909) was recorded at both DRE and NWB. The known range of Dynamena nanshaensis (Tang, 1991), recorded for the second time, is extended further north. Six species (Aglaophenia latecarinata, Plumularia floridana, Diphasia palmata, Dynamena brevis, Dynamena obliqua, Synthecium elegans) are recorded for the first time in waters adjacent to the Chinese mainland. Conclusions: Species composition and abundances varied considerably from one environment to another and especially between DRE and NWB. This study provides the first taxonomic account of the hydroid fauna inhabiting the eastern Taiwan Strait region.