Influenza A virus causes respiratory disease in both humans and animals. In this study, a survey of influenza A antibodies in domestic dogs and cats was conducted in 47 animal shelters in 19 provinces of Thailand from September 2011 to September 2014. One thousand and eleven serum samples were collected from 932 dogs and 79 cats. Serum samples were tested for influenza A antibodies using a multi-species competitive NP-ELISA and haemagglutination inhibition (HI) assay. The NP-ELISA results showed that 0.97% (9/932) of dogs were positive, but all cat samples were negative. The HI test against pandemic H1N1, human H3N2 and canine H3N2 showed that 0.64% (6/932) and 1.20% (1/79) of dogs and cats were positive, respectively. It is noted that all six serum samples (5 dogs and 1 cat) had antibodies against pandemic H1N1. In summary, a serological survey revealed the evidence of pandemic H1N1 influenza exposure in both dogs and cats in the shelters in Thailand.