The genetic relationships among Euglena strains remain poorly understood, despite a rich history of morphological examination and an extensive phylogenetic analysis of the ribosomal RNA genes. It is difficult to identify related species of the genus Euglena and to separate different strains of the same species because the morphological characters are variable and limited. We address this question using microsatellite DNA fingerprinting. Seven microsatellite loci were amplified from 7 Euglena strains. A total of 4-8 bands were successfully amplified for each of 6microsatellite primer pairs. Microsatellite DNA fingerprinting and similarity values ranging from 0.000 to 0.957 a-mong the seven strains were obtained, which were used to construct a similarity tree among them. According to the tree, at the linkage distance of 0.9346 seven strains were separated into three clusters: E. mutabilis, E. intermedia and E. gracilis consisting of Japanese and USA groups. Further, in the cluster E. gracilis, different genotypes were recognized for the strains from different geographical origins. The relationships among species and strains were analyzed preliminarily. We demonstrates that the seven strains of Euglena can be clearly separated by their microsatellite DNA fingerprinting patterns. The microsatellite DNA fingerprinting has a high resolution and is a new useful method to identify and separate similar species and intraspecific strains in free-living protozoa.