Objective Clostridium sp. isolation， identification and analysis and toxin gene detection were carried out on 57 pieces of commercially available infant formula milk powder and 50 pieces of commercially available infant rice noodles sold in Beijing. The data of Clostridium sp. contamination level was obtained， and the identification methods were evaluated.Methods The isolates were comprehensively identified by their growth characteristics， Gram staining， morphological characteristics under ordinary microscopy， combined with the results of mass spectrometry identification， 16S rRNA gene sequencing and whole-genome sequencing （WGS）. The botulinum toxin genes of isolated Clostridium sp. were detected by PCR. Then， sequencing and comparative analysis of PCR positive fragments were carried out.Results Thirty-eight Clostridium sp. in 26 samples of the 57 commercially available infant formula milk powder samples were detected. More than two types of isolates were detected in 9 samples. Five Clostridium sp. were detected in 5 samples of 50 commercially available infant rice flour. PCR amplification of the Clostridium botulinum type E toxin gene of a Clostridium sphenoides was positive， the amplified fragment sequencing comparison results showed that this sequence was not an E-type Clostridium botulinum toxin gene， and the WGS results also confirmed it. There were no toxin genes of Clostridium botulinum in all the 43 isolates.Conclusion Identification of Clostridium sp. requires comprehensive analysis by multiple methods. The contamination of Clostridium sp. exists in commercial infant formula milk powder and infant formula rice flour. It is necessary to strengthen the monitoring of important Clostridium sp. in infant formula food to provide data support for risk assessment.