Since 2001, a glass American eel, Anguilla rostrata (Lesueur), survey has been conducted at Guana River Dam, Florida, USA. Although present in earlier samples, glass speckled worm eel, Myrophis punctatus Lütken, were not identified until a large proportion appeared in samples in 2006. To determine whether the species could be separated in historical samples, weight–length relationships were compared between the two species. Then, with data from the full survey period, relationships between catch rate and annual percent contribution of glass speckled worm eel were explored in relation to temperature, water flow and salinity. Glass speckled worm eel were found to weigh significantly less and had distinguishing physical characteristics that could be used for identification. Glass speckled worm eel constituted between 0 and 34% of the catch, with no detectable pattern in timing or abundance among years. In 2006 and 2012, which had the two largest catches of glass speckled worm eel, relationship between nightly catch rate and measured environmental variables was inconsistent, even when measured variables had a similar range in values. It is recommended that south‐eastern, including Gulf of Mexico, USA, states restrict harvest of glass American eel to prevent the incidental capture and exportation of glass speckled worm eel. Efforts should be made to ensure proper species identification in glass eel surveys.