Clostridium perfringens presents persistent threat to small animals in causing moderate to severe enterotoxemia. The pathogenicity of C. perfringens depends on the production of four major toxins. In addition to the major toxins, beta2 (β2) toxin, a minor toxin, is also produced by some strains of C. perfringens. In this study, a total of 107 fecal samples collected from healthy and diseased sheep and goats were cultured and processed for biochemical analysis. On the basis of biochemical characterization, 61 isolates were confirmed as C. perfringens. In order to detect C. perfringens types, multiplex PCR assay was carried out for the confirmed isolates. Results indicated that the gene encoding beta2 (β2) toxin was found in 73% of type A isolates and 67% of type D isolates. There was no significant difference in the presence of this gene in the sheep and goats. An association between beta2 (β2) gene and disease occurrence was also found non-significant in both sheep and goat species. The present study suggests the high prevalence of C. perfringens beta2 gene (β2) in fecal isolates of both sheep and goats. However, the role of beta2 (β2) toxin gene in pathogenesis of enteric diseases needs further investigations.