In order to identify the pathogenic agents prevalent in a farm with diseased pigs in Chongqing City and to determine their characteristics of biology and molecular evolution，the tissue samples were detected by PCR，and it was found that two kinds of pathogens including Haemophilus parasuis（Hps）and circovirus type 3（PCV3）were positive. Followed by bacteria isolation as well as identification by morphology，culture characteristics and 16S rDNA sequencing，then their serotype，drug sensitivity，drug-resistance genes，growth curve and other major biological characteristics were analyzed. It was determined that the pathogenic strain was Hps serotype 5，the isolate was resistant to ceftazidime，oxacillin，neomycin，kanamycin，chloramphenicol，minocycline，polymyxin B and tetracycline，and a total of nine drug-resistance genes were detected；PCV3 complete genome sequence was obtained by segmental amplification and splicing，then its gene structure and genotype were analyzed by the biological software. It was found that the total length of PCV3 genome was 2 000 bp，the GC content was 50.45%，and the genotype was PCV3a，which was highly close to Guangxi MH823221 strain and KT869077 strain firstly reported in the United States. In conclusion，the pathogens in the diseased pigs and its major characteristics of biology and molecular evolution were determined，which provided a basis for future effective prevention and control of mixed infection with Hps and PCV3 in practice.