Objective To provide the basis for plague prevention and control by investigating species composition and infection rate of Yersinia pestis in fleas collected from floor in the plague natural foci of Lijiang in Yunnan province. Methods Investigation was carried out at 8 villages of Yulong county and 5 villages of Gucheng district of Lijiang. Floor fleas were collected by sticky flea paper method. Species was identified based on morphological characteristics. Y. pestis was cultured from fleas in laboratory. Results The sticky flea paper 21 845 copies were collected in the 13 villages. The average flea index of 0.0249. The sex ratio of fleas was 1.95:1. In total, 545 fleas were collected, which belong to 2 families, 3 genera and 3 species, including Ctenocephalides felis felis (69.54% ), Pulex irritants (18.72% ), and Ctenophthalmus quadrarus (11.74%). Infection of Y. pestis was negative for all fleas. Conclusion There are 3 flea species from floor in the plague focus, Ct. felis felis, P. irritant were predominating species. Infection of Y. pestis was not found.