Microbial degradation of aromatic hydrocarbons is an emerging technology, and it is well recognized for its economic methods, efficiency, and safety; however, its exploration is still scarce and greater emphasis on cyanobacteria–bacterial mutualistic interactions is needed. We evaluated and characterized the phenanthrene biodegradation capacity of consortium dominated byFischerellasp. under holoxenic conditions with aerobic heterotrophic bacteria and their molecular identification through 16S rRNA Illumina sequencing. Results indicated that our microbial consortium can degrade up to 92% of phenanthrene in five days. Bioinformatic analyses revealed that consortium was dominated byFischerellasp., however different members ofNostocaceaeandWeeksellaceae, as well as several other bacteria, such asChryseobacterium, andPorphyrobacter,were found to be putatively involved in the biological degradation of phenanthrene. This work contributes to a better understanding of biodegradation of phenanthrene by cyanobacteria and identify the microbial diversity related.