In order to avoid the influence of associated bacteria on the target cyanobacteria for physiological and molecular studies, a traditional and reliable method based on solid-liquid alternate cultivation is carried out to purify the non-axenic cyanobacterium Microcystis aeruginosa FACHB-905. On the basis of 16S rDNA gene sequences, two associated bacteria named strain B905-1 and strain B905-2, are identified as Pannonibacter sp. and Chryseobacterium sp. with a 99% and 97% similarity value, respectively. To better investigate the general interaction between the bacterium and the cyanobacterium, the effect of strain B905-1 on the axenic cyanobacterium M. aeruginosa FACHB-905A is studied. Results indicate that the axenic M. aeruginosa FACHB-905A could not form colonies on BG11 agar medium without the addition of strain B905-1, while it grows well in BG11 liquid medium. Although the presence of B905-1 was not indispensable for the growth of M. aeruginosa FACHB-905A, B905-1 had a positive effect on promoting the growth of M. aeruginosa FACHB-905A. The purification technique for cyanobacteria described in this study is potentially applicable to a wider range of filamentous cyanobacteria.