Objective To provide the basis for plague prevention and control by investigating in the flea species from dog and cat and infection rate of Yersinia pestis in the plague natural foci of Lijiang in Yunnan province. Methods Investigation was carried out at 3 villages of Yulong county and 3 villages of Gucheng district of Lijiang. Fleas on dog body and cat body were collected with insecticide bath, and identified based on morphological characteristics. Y. pestis was cultured from fleas in laboratory. Results There 93 dogs were investigated and there were fleas on 74 dogs, with average fleas infection rate is 79.57%, average fleas index is 2.63. Totally 245 fleas were collected from dog, and all are Pulex irritans. The sex ratio of fleas was 2.14:1. There were fleas on 28 of 37 investigated cats, average fleas infection rate is 75.68%, average fleas index is 2.46. Totally 91 fleas were collected, including P. irritans (46.15%), Ctenocephalides felis felis (53.85%). The sex ratio of cat fleas was 3.55:1. Infection of Y. pestis was negative for all fleas. Conclusion The P. irritans were predominat species to dog body fleas, P. irritans and C. felis felis were predominating species to cat body fleas. Infection of Y. pestis was not found.