Mycoplasma hyopneumoniae (M. hyo) causes significant losses to the economy of the pig industry in the world. Little information is available about the prevalence of M. hyo infection in Chinese native pigs. We report herein a high seroprevalence (61.5%) to M. hyo in Chinese native pigs (Meishan and Fengjing) from Shanghai, China. Meishan or Fengjing pigs had a significantly higher seroprevalence compared to Duroc × Landrace × Yorkshire pigs (p < 0.05). Among Meishan and Fengjing groups, the peak prevalence was in breeding pigs (74.5%), followed by suckling piglets (71.4%), finishing pigs (69.6%) and nursery pigs (34.7%) and differences were statistically significant (p <0.05). PCR analysis of the nasal swabs showed that 5.1% (5/98) of the Meishan pigs (6.5%,3/46) or Fengjing pigs (3.8%,2/52) were positive for M. hyo. The nucleotide sequences of p46 genes of M. hyo from Meishan pigs or Fengjing pigs were highly conserved with 98.6-99.8% sequence homology with other reference strains. Our data confirm that M. hyo infection in native pigs was highly prevalent in Shanghai, and thus integrated strategies should be taken to control the disease.