Changes in algal and bacterial communities during thiocyanate (SCN-) decomposition in a microalgamediated process were studied. Pyrosequencing indicated that Thiobacillus bacteria and Micractinium algae predominated during SCN- hydrolysis, even after its complete degradation. Principal components analysis and evenness profiles (based on the Pareto-Lorenz curve) suggested that the changes in the bacterial communities were driven by nitrogen and sulfur oxidation, pH changes, and photoautotrophic conditions. The populations of predominant microalgae remained relatively stable during SCN- hydrolysis, but the proportion of bacteria - especially nitrifying bacteria - fluctuated. Thus, the initial microalgal population may be crucial in determining which microorganisms dominate when the preferred nitrogen source becomes limited. The results also demonstrated that microalgae and SCN--hydrolyzing bacteria can coexist, that microalgae can be effectively used with these bacteria to completely treat SCN-, and that the structure of the algal-bacterial community is more stable than the community of nitrifying bacteria alone during SCN- degradation.