Tropical species of anguillid glass eels have recently been exploited to be a substitute for the commercially important Anguilla japonica or A. anguilla, so information about their life histories is needed to facilitate conservation. To understand ecological aspects of glass eel recruitment patterns of tropical eels, Anguilla spp., monthly monitoring of species compositions at the mouth of the Cagayan River in northern Luzon in the Philippines was carried out at different time periods from May 2008 to September 2009 and from November 2011 to December 2012. Species identifications were made for 32,178 glass eels using morphology and/or genetics, and a total of five anguillid species, Anguilla bicolor pacifica, A. celebesensis, A. japonica, A. luzonensis, and A. marmorata, were found. In both time periods A. marmorata was dominant followed by A. luzonensis and A. bicolor pacifica, but the proportion of A. marmorata decreased from 55.1% in 2008–2009 to 41.2% in 2011–2012, with A. bicolor pacifica increasing from 3.9% to 26.3% and A. luzonensis staying relatively stable (41.0%, 32.5%). Two other species, A. japonica and A. celebesensis, that were reported in previous studies from the Cagayan River were extremely rare. This study indicated that selective glass eel catch of a commercially preferred tropical species in this area is not feasible, because the harvest will include a high proportion of bycatch of economically less-important species, potentially having considerable impacts on their populations.