Population genetic structure and evolutionary scenario were investigated with the microsatellites analysis for three species of the freshwater eels, tropical Anguilla reinhardtii (Steindachner 1867), and temperate Anguilla australis (Richardson 1841) and Anguilla dieffenbachii (Gray 1842) in Australia and New Zealand. A total of 1277 glass eel specimens were used: 388 from East Australia and New Zealand for A. australis, 90 from both North and South Island of New Zealand for A. dieffenbachii, and 799 from East Australia for A. reinhardtii, including a series of monthly collections for over 12 months from the Albert River estuary. The specimens were collected from East Australis in 1997-1999 and New Zealand in 1995-1996. For A. reinhardtii there was no significant spatial and temporal differentiation in the genetic structure. This may be due to the fact that it has a short pelagic larval duration, narrow distribution range, but a long, all the year round spawning period, that facilitate the gene flow. For A. australis that has comparatively longer pelagic larval duration than that of A. reinhardtii, two geographical populations were recognized in East Australia and New Zealand, respectively. For A. dieffenbachii in New Zealand that has the longest duration of the pelagic larval stage has no population genetic differentiation due to the small land mass for dispersal. A. dieffenbachii is characterized with more ancient morphological and genetic characters than the A. australis in the same evolutionary lineage. These may suggest that temperate eel A. dieffenbachii is the earliest arrival of the freshwater eel in Oceania. Genetic variation in microsatellite loci may provide a useful tool in examining evolution and population dispersal of freshwater eels.