Fine structure and elemental composition of envelopes of 10 taxa of Trachelomonas and Strombomonas from natural freshwater bodies in China were studied and phylogeny of both genera were discussed. The results indicate that iron (Fe) and silicon (Si) are the primary mineral elements of the envelopes. Composition of mineral elements was uncorrelated with envelope color, however, it was highly correlated with the microarchitecture of the envelopes. Content of Si was higher than that of Fe in all species of Strombomonas and some species of Trachelomonas with rough surface. In most species of Trachelomonas, especially those with dense and smoothy surface, content of Fe was higher than that of Si. Based on the above results, we propose to assign those species of Strombomonas into Trachelomonas and consider them as a group of the latter. These species were the most primitive among the group with envelopes in Euglenaceae.