Clostridium perfringens is a Gram-positive, anaerobic bacterium linked to various diseases in humans and animals, particularly necrotic enteritis in ovine and caprine species. Typically, researchers use its toxins to systematically classify isolates into seven toxinotypes (A-G) based on their presence or absence. Using microbial culture, microscopic examination, and specific primers, this study was conducted to identify major and secondary toxins, their isolation sources, and their clinical association with sheep necrotic enteritis. Between September 2023 and June 2024, 85 isolates of C. perfringens bacteria were isolated from 250 sheep samples. The PCR results revealed that the cpa and plc genes were present in all samples, and the cpe and etx genes were present in 20 bacterial isolates, accounting for 23.53%. The major toxinotypes in local clinical cases were Type A (65/85, 76.5%) and type D (20/85, 23.53%). Type A cases comprised 20 lambs and 45 adult sheep, whereas all type D cases were from adult animals. The sequence analysis of partial 16S rRNA sequences demonstrated different degrees of similarity with sequences of other C. perfringens strains recorded in GenBank from Iraq and other countries. However, the local isolates clustered together, indicating a strong ancestral connection. These findings suggest the necessity for the integration of toxinotypes A and D into sheep vaccination programs and the pursuit of comprehensive epidemiological studies on the toxinotypes in humans and animals.