Bioremediation of crystal violet and ammonia was investigated by Spirulina (Arthrospirafusiformis) in aquatic system.As well as, studying effect of crystal violet against genetic structure of Spirulina using biochemical and molecular genetic techniqes was the other aim of this study. Spirulina was capable of using crystal violet and ammonia as sole sources of carbon and nitrogen, respectively.Crystal violet and ammonia were completely remediated by Spirulinain liquid medium at pH 9 and 35 °C after 25 incubation days comparing with uninoculated medium (control). No toxicity of crystal violet was appeared after 25 days of incubation with A. fusiformisandBacillus subtilisE5 as a microbial bioassay test. The dissipation of crystal violet and ammonia was coinciding with increasing A. fusiformis biomass. Estraseenzyme activity and RAPD analysis wereappliedin order to study thegenotoxic effect of crystal violet on genome structure of Spirulina. Enzyme activity of estrase was markedly differed in crystal violet treated algae in comparison with control group, indicating theinhibition of enzyme activity as bands number andhigh polymorphism percentage(87.5%) between control and treatment. Seven RAPD primers generated 44 DNA fragments, 37of them were polymorphic (84.09%).The results indicated that crystal violet induced genotoxic effect on the genomic structure of Spirulina.So, it is worth to conclude thatA. fusiformis could be applied to remediate crystal violet and ammonia contaminated water.