The development of serotyping-based diagnostic methods and multivalent vaccines has been significantly hampered due to the limited information available on the genetic differences among the 15 currently known serotypes of Actinobacillus pleuropneumoniae. In this study, using the GenomeComp informatics software, differential genes were screened and identified between the complete genome sequences of the serotypes 5b (L20 strain, highly virulent) and 3 (JL03 strain, weakly virulent), 84 presented uniquely in strain L20, while 57 were only found in JL03 strain. Of these, 75 encode putative proteins and 66 encode hypothetical proteins, including phage-related proteins, Apx toxin, capsular polysaccharide biosynthesis proteins, ATP-binding cassette (ABC) transporters, Clp-like proteases, fimbrial protein (Flp), various glycosyltransferases, methylases, integrases, and other proteins related to virulence. To confirm and further characterize the differential genes, we carefully selected 34 proven or putative virulence genes which were extremely useful on researching into detection and vaccine of A. pleuropneumoniae, and investigated the distribution and transcription of these genes among the 15 serotypes through polymerase chain reaction, reverse transcriptase- polymerase chain reaction and sequencing, and different distribution and transcription patterns of the differential genes in each serotype were first found and described. These information of these differential genes among the 15 serotypes of A. pleuropneumoniae may greatly serve as an indicator for future research on the pathogenic mechanisms of different serotypes, serotyping-based diagnostic methods, and multivalent vaccines.