One hundred and seven chickens or silky chickens were tested for infectious bronchitis virus between August 2003 and December 2005 in Guangdong and Hunan Chinese provinces, from which SARS coronavirus has initially emerged. IBV was detected in 82 birds (prevalence: 77%). Limiting the IBV detection PCR to tracheal or cloacal swabs would have led to a considerable underestimation of virus prevalence of 50 to 66% only. 15 sequences of 362 bp of the spike 1 gene (S1) were obtained. 13 strains clustered with Chinese genotype IV strains, which were recently reported in South China too. Genotype IV also showed the larger evolutionary distances in comparison to other Chinese genotypes. IBV/CK(T)/GD.CH/05-04/3587 strain clustered with genotype III virus, showing that genotype III continues to circulate in Guangdong province at least. A vaccine strain was probably detected in a bird as IBV/CK(C)/HN.CH/05-06/2904 was identical to H120 and H52 vaccines which are commonly used in Chinese poultry farms. It is nevertheless not likely that the IBV strains which could not be sequenced were vaccine strains: since both detection and sequencing PCRs were equally sensitive for the vaccine strain, sequencing would rather overestimate vaccine strains than wild-type variants. Our results suggest that at life-bird markets almost all birds carry wild-type IBV and that these markets may be an important and so far underestimated source of infection for IBV.