The PCR analysis of the mitochondrial 16S ribosomal RNA partial sequence was used to identify the eel species in the surrounding waters of Taiwan. In total, 802 elvers were sampled from December 2009 to March 2012, and the 16S rRNA sequence data for these samples was compared to the NCBI database. The results showed 4 species, among which giant mottled eel, Anguilla marmorata were most abundant, followed by Indian short-finned eel, A. bicolor pacifica and Luzon mottled eel, A. luzonensis. Only one sample was identified as an Indonesian mottled eel, A. celebesensis. This occurrence of an Indonesian mottled eel in the surrounding waters of Taiwan is the first record identified by 16S rRNA sequencing.