[Objective] The aim of this study is to analyze bacterial community and antibiotic resistant genes (ARGs) in organic, fertilized and wild Houttuynia cordata Thunb, and to reveal the relationship between bacterial community and ARGs. [Methods] The bacterial community structure was investigated by high-throughput 16S rRNA V3-V4 variable region sequencing. The qualitative and quantitative analysis of 29 ARGs was determined by PCR and qPCR. The redundancy analysis was used to reveal the relationship between bacterial community and ARGs. [Results] A total of 35 genera of bacteria were detected. The bacterial diversity in organic H. cordata Thunb was lower than that in fertilized and wild H. cordata Thunb. Fourteen ARGs were detected on H. cordata Thunb. All detected ARGs were found in the organic H. cordata Thunb, while only part was found in the fertilized and wild H. cordata Thunb. Redundancy analysis showed ARGs were significantly affected by bacterial diversity and abundance, and Lactococcus, Escherichia, Fluviicola, Enterococcus, Sanguibacter and Acidovorax were main bacteria which affected on the diversity and abundance of ARGs on H. cordata Thunb. [Conclusion] Organic planting affects bacterial community on H. Cordata Thunb, and increases diversity and abundance of ARGs, suggesting a potential food safety risk. Therefore, it is necessary to bring ARGs contamination into the scope of food safety assessment for organic H. cordata Thunb.