This study analyzed the population structure and habitat use of the Japanese eel (Anguilla japonica) and the marbled eel (Anguilla marmorata) in the Pearl River based on data collected from 2015 to 2018. A total of 181 Japanese eels and 56 marbled eels were collected, over half of which were middle-sized eels between 255 and 600 mm in length. Although they are sister species, Japanese eels mainly inhabit complex river habitats characterized by high river fractals and coefficients of fluvial facies, while marbled eels mainly inhabit wider and deeper river sections. The results of this study showed that wild Anguilla spp. resources in the Pearl River were extremely low and there was an urgent need for conservation and management of eel resources in south China.