Based on the 16S rRNA gene sequence of chloroplasts, this study constructed the phylogenetic tree of green euglenophyte and reconstructed their ancestor on the base of 8 morphological characters, which will clarify the phylogenetic relationships of green euglenophyte and provide theoretical basis for the study of the origin of these plants. The results indicated: (1) the phylogenetic tree of green euglenophyte constructed by Bayesian showed that Eutreptia and Eutreptiella are sister groups, and Phacus, Lepocinclis and Discoplastis are close relatives. We also can see that Trachelomonas and Strombomonas are close relatives, and Euglena, Cryptoglena, Colacium and Monomorphina have close genetic relationships. It is showed that Euglena is not a monophyletic group. (2) The results of ancestral reconstruction based on morphological characters showed that 7 relatively original characters of green euglenophyte included: cuticula soft and easy deformation, spirally striated, posterior end slightly narrowing or sharp elongated cauda, without lorica, chloroplasts show sheet, shield, or plate, pyrenoid without sheath, with many small grains are primitive traits, but the length of flagella can not infer possible ancestral states. (3) The results of ancestral reconstruction based on 8 morphological characters showed that Euglena and Euglenaria which have original characters may be the ancestor of green euglenophytes who appear earliest.