Detection of microsporidia at the species level is important for therapeutic purpose. The available techniques, modified trichrome (MT) staining cannot differentiate between species, while polymerase chain reaction (PCR) requires a reference laboratory and skilled technical staff. Immunoflourescence antibody (IFA) assay is another technique, which can differentiate among commonest species of microsporidia. However, there are very limited studies on its efficacy worldwide. Therefore, we aimed to evaluate IFA assay for the detection of microsporidia and differentiation among commonest species, Enterocytozoon bieneusi (E. bieneusi) and Encephalitozoon intestinalis infecting immunocompromised patients. Stool samples from 200 immunocompromised patients (19 with microsporidia and 181 without microsporidia using MT staining) were tested for species identification by PCR-RFLP and IFA assay. Sensitivity, specificity, diagnostic accuracy, and positive and negative predictive values were calculated as per standard formulae. Kappa statistics was used to assess the agreement between three tests. Of 200 immunocompromised patients, 21 and 20 patients had microsporidia using PCR and IFA assay, respectively. IFA assay and PCR identified E. bieneusi in all patients infected with microsporidia. Considering MT stain as gold standard, sensitivity and specificity of IFA assay was 100 and 99.4 %, respectively. Upon considering PCR as gold standard, sensitivity and specificity of IFA assay was 95.2 and 100 %, respectively. Diagnostic accuracy of IFA assay was 99.5 % along with its high test agreement with MT staining and PCR (K = 0.915, p = 0.049; K = 0.973, p = 0.027). IFA assay is highly sensitive and specific technique for detecting and identifying species of microsporidia among immunocompromised patients. E. bieneusi was the commonest species identified.