Eel family is a huge one, in which many kinds of eels especially some migratory eels, bear strong resemblance to each other, and are therefore difficult to be identified. In this study 29 random primers were used to make RAPD analysis for Japanese eel (Anguilla japonica), European eel (Anguilla anguilla) and Pike eel (Muraenesox cinereus). And totally 299 fragments were counted. Shared or specific fragments were counted and genetic similarity or genetic distance were calculated. The genetic similarity between Japanese eel and Pike eel is 0.68 and the genetic distance between them is 0.32; those between European eel and Pike eel are 0.72 and 0.28 respectively, and between Japanese eel and European eel are 0.74 and 0.25 respectively. The method has been shown to be suitable to molecular identification of eels. It provides an alternative approach to determine the relationship between species.