The aim of the study is to determine the occurrence of the genes coding for toxins produced by Clostridium perfringens isolates, recovered from 392 samples of herbs and spices, including alpha (cpa), beta (cpb), epsilon (etx), iota (iA) and enterotoxin (cpe) using polymerase chain reaction (PCR) and randomly amplified polymorphic DNA (RAPD) assay. The results revealed that 33 samples (8.42%) were positive for C. perfringens. Multiplex PCR using 5 primers for the examined toxin-encoding genes revealed that isolates possess genes of alpha (cpa; 100%; 33 out of 33), beta (cpb; 30.3%; 10 out of 33), epsilon (etx; 6.06%; 2 out of 33), iota (iA; 0.0%; zero out of 33) and enterotoxin (cpe; 15.15%; 5 out of 33), indicating that the isolates were all toxigenic with the exception of iA toxin. Conducting RAPD assay using short random primers revealed similar results confirming our data with overall Jaccard/Tanimoto coefficient of 0.26. Sequencing analyses of cpa gene was performed as the alpha toxin-encoding gene was detected in 100% of samples. Our study provides data for the occurrence of genes coding for different toxins as virulence factors possessed by C. perfringens, isolated from herbs and spices distributed in Egyptian markets. The data recommend applying strict hygienic and sanitary measures in foods containing the additives examined.