Glass eels migrating upstream in a New Zealand river showed a clear preference for water temperatures between 12 and 20°C, with an optimum of 16.5°C. Water temperatures <12°C and >22°C almost completely inhibited migration, which implies that warmer temperatures associated with global climate change might have a detrimental impact on glass eel recruitment in their current ranges. We established this by trapping glass eels of shortfin, Anguilla australis, and longfin, A. dieffenbachii, eels nightly from September to November. Eels caught in 2001 (50,287) outnumbered those caught in 2002 (19,954); shortfin glass eels dominated catches in both years, comprising 91–93% of the catch. Longfins were larger than shortfins, and size and pigmentation in both species increased as the seasons progressed. Temperatures within the migratory season in 2001 showed ∼14-day intervals between maxima that appeared to be associated with the new and full moons.