Blastocystis is a highly controversial protozoan parasite. It has been variably regarded as a commensal and pathogen. Scientists have for decades wondered whether it is truly an enteropathogen and if it is observed in symptomatic patients whether treatment is required because patient recovery and improvement has been noted even without any treatment. Though associated with self-limiting infection, treatment is warranted in many patients due to persistence of symptoms. This particularly holds true for children and adults who are immuno compromised. Several drugs have been used to treat Blastocystis but each one of them has produced widely variable rates of clinical cure and eradication of the parasite from the feces. Based on the studies carried out in vitro and clinical responses obtained in patients, metronidazole appears to be the most effective drug for Blastocystis infection. However, the therapy is complicated due to different dosages and regimens adopted and the unresponsiveness to treatment observed in several sections of the population studied. Recently, the finding of different subsets of Blastocystis exhibiting resistance to metronidazole and associated with variable degrees of symptoms has underscored the importance of typing the subsets of the parasite in order to foretell the clinical response and the need to treat. Till date, the mode of action of the drugs used and the mechanism of resistance is not entirely known and is a topic of speculation. Other drugs with anti Blastocystis activity and used in therapy includes trimethoprim sulfamethoxazole and nitazoxanide. Several other compounds have also been evaluated for the treatment either alone or in combination with the first or second line drugs. A lot of interest has also been generated on the role of probiotics particularly Saccharomyces boularrdii and other natural food compounds on eradication of the parasite. This review provides a comprehensive overview of antimicrobials used to target Blastocystis and discusses the issues pertaining to drug resistance, treatment failure, reinfection, and the current views on treatment modalities.