Clostridium perfringens is a zoonotic pathogen causing various health problems like gas gangrene, food poisoning, and other enteric infections, especially in domestic livestock, leading to significant global economic losses. In present study, C. perfringens strains were isolated and identified depending on 16 rRNA and genotyping based on genes encoding alpha, beta, epsilon, iota, enterotoxin, NetB toxins, then sequencing of 16S rRNA and some main toxin-producing genes in 219 samples collected from domesticated ruminants in sheep, goats, and calves, during the period from August to December of 2020, in Duhok province/ Iraq. Out of a total 67, Forty-seven (28.8%) isolates of C. perfringens were obtained in 163 ruminal content samples from healthy sheep and goats, and out of 56 samples of calves (34 healthy and 22 diarrheic); 20 (35.7%) isolates (7 (20.5%) isolates from healthy and 13 (59%) isolates from diarrheic) were confirmed as C. perfringens. Of the 47 isolates from healthy sheep and goats, 39 (82.97%) were identified as type A, and 8 (17.03%) as type D. While all 20 isolates from healthy and diarrhetic calves were diagnosed as type A.  None of the total 67 C. perfringens isolates were carrying genes encoding beta, iota, enterotoxin, and NetB toxins. Phylogenetic tree analysis revealed that all isolated strains were clustered in same group. Clostridium perfringens is one of the major pathogens with health concern in both humans and animals. Type A and D were the only genotypes obtained from the collected samples which were genetically similar.