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• C. perfringens was found in 23.4 % of chickens and 72.0 % of pigs. • All 322 C. perfringens isolates belonged to toxin type A and 45.7 % carried beta-2 toxin-encoding gene cpb2. • Most strains showed high-level resistance to gentamicin and sulfonamides, and low resistance to amoxicillin-clavulanate and cephalosporins. • Genetic diversity was observed and high nucleotide sequence identity to C. perfringens plasmids suggested that horizontal gene transfer may occur. • Isolates from the same farms and areas were found to be phylogenetically close. The prevalence and antimicrobial susceptibility of Clostridium perfringens (C. perfringens) in chickens and pigs were investigated in Beijing and Shanxi, China. In total, 322 C. perfringens (chicken n = 60 and pig n = 262) were obtained from 620 feces of chickens (n = 256) and pigs (n = 364). Multiplex PCR for toxin typing of C. perfringens revealed that all the isolates belong to type A, with 45.7 % (147/322) isolates carrying beta-2 toxin-encoding gene cpb2. Minimum inhibitory concentrations of 27 antimicrobial agents showed that 91.0 % of the tested C. perfringens isolates were resistant to gentamicin and sulfonamides (sulfisoxazole and trimethoprim-sulfamethoxazole), and little resistance was showed to amoxicillin-clavulanate, ceftiofur, doxycycline, vancomycin and linezolid. Additionally, nosiheptide, avilamycin, virginiamycin and bacitracin exhibited good activity against the tested C. perfringens with low MIC 50 (0.06 to ≤4 μg/mL) and MIC 90 values (0.25–8 μg/mL). Whole genome sequencing (WGS) of 48 representative isolates from each farm indicated that the C. perfringens contained diverse antimicrobial resistance genes [ tetA (P), ant(6)-Ib , erm (Q), etc.] and toxin genes (cpb2 , colA , cloSI , pfoA , etc.). By comparative analysis, four C. perfringens isolates from three different pig farms harboured cpb2 -carrying plasmid p1 with 100 % nucleotide sequence identity, suggesting horizontal gene transfer among these microorganisms. The further phylogenomic reconstruction, based on the core-genome single nucleotide polymorphisms (SNPs) of the representatives, demonstrating that C. perfringens from the same farms and regions were closely related. These findings expanded our knowledge of C. perfringens isolated from animals in China, which provided scientific basis for efficient intervention or prevention measures of antimicrobial resistance in animal husbandry in China. [ABSTRACT FROM AUTHOR]