Simple, sensitive and rapid methodology was developed for the separation and identification of selenium(IV) and cobalt(II) in Macrobrachium lamarrei, fresh water prawn samples and their feeding materials after pre-capillary complexation with ammonium piperidine-1-carbodithioate (APC) by using capillary electrophoresis. Microwave assisted procedure was adapted to analyze selenium(IV) and cobalt(II) in prawn samples which was eco-friendly to environment. Various parameters such as effect of pH, effect of complexing agent concentration, buffer nature, applied voltage and interferences by other metal ions were also investigated to enhance the sensitivity and detection limits of the present method. The obtained results were in good agreement and correlated with AAS method in terms of Student's “t”-test and Variance ratio “f”-test. The method was applied for the analysis of selenium(IV) and cobalt(II) in various M. lamarrei, fresh water prawn samples and their feeding materials.