Blastocystis sp. is an enteric protozoan parasite of humans and many animals. Blastocystis sp. subtype 3 (ST3) proves to be the highest frequency case in most populations around the world and it is further distinguished into symptomatic and asymptomatic isolates based on the clinical symptoms exhibited by infected individuals. Phenotypic and genotypic studies implicate the distinctiveness of this parasite which may describe its pathogenesis. However, the antigenic distinctiveness which describes the antibody mediated cell lysis of this parasite has not been explored. This study was aimed to identify the cross-reactivity and cytotoxicity effect between three isolates of symptomatic and asymptomatic Blastocystis sp. ST3 respectively. Antigen specificity and diversity of this parasite was performed by coculturing sera (10-fold dilution) obtained from mice immunised with Blastocystis sp. symptomatic and asymptomatic antigens and the respective Blastocystis sp. ST3 live cells through complement dependant cell cytotoxicity (CDC) assay. The results obtained has shown that, the sera (at 10-fold diluted concentration) from symptomatic and asymptomatic solubilised antigen immunised mice were able to specifically lyse the respective live parasites with an average percentage of 82% and 86% respectively. There were almost 50% crossreactivity observed between the three isolates of Blastocystis sp. ST3 from symptomatic and asymptomatic group proving high antigen diversity or rather low antigen specificity within the same group. However, there was only 17% cross-reactivity observed between the mice sera and parasitic cells of different groups (symptomatic vs asymptomatic isolates) suggesting high specificity between these two groups. We, for the first time have proven that through CDC analysis there were epitopes dissimilarities between Blastocystis sp. ST3 symptomatic and asymptomatic isolates which may allow the parasite to set up diverse immune modulations such as imbalanced Th1/Th2 responses in an infected host.