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Accurate differentiation and identification of flea species are essential for both basic and applied research on fleas, as well as for the diagnosis of flea-borne diseases. However, distinguishing between flea species can be challenging, especially among those with minimal morphological differences. Therefore, some scholars have suggested the necessity of comprehensive revisions to the classification of fleas, incorporating morphological, molecular, and phylogenetic data. In this study, we focused on classifying the rodents' parasitic fleas in southeastern China and provided molecular and phylogenetic data. We also described a new subspecies Ctenophthalmus breviprojiciens fujiansis n. ssp. A total of 392 fleas were collected from 8 species of rodents in 10 counties. Morphologically, they belonged to 10 species, 9 genera and 5 families. Barcode identification based on COI gene and phylogenetic analysis based on five genetic markers (18S rDNA, 28S rDNA, EF-1a, COI, COII) revealed that the molecular and morphological identification of Xenopsylla cheopis, Aviostivalius klossi bispiniformis, Leptopsylla segnis, Monopsyllus anisus and Ctenocephalides felis felis were consistent. The taxonomic status of Neopsylla specialis minpiensis and Peromyscopsylla himalaica sinica as subspecies is questionable due to significant intraspecific genetic distance, and further morphological and molecular data are required to determine if they should be elevated to species level. The molecular identification of C. breviprojiciens n. ssp., N. dispar fukienensis, and Nosopsyllus nicanus could not be completed at this time due to a lack of sequences for related species in existing GenBank databases. Additionally, phylogenetic relationships of 31 species from 9 genera and 5 families of Siphonaptera were inferred based on five molecular markers (18S rDNA, 28S rDNA, EF-1a, COI and COII) using Maximum Likelihood analyses. The analyses revealed that various taxa of Siphonaptera are monophyletic at the subspecies, species, and genus levels. However, at the family level, Leptopsyllidae, Ceratophyllidae, Pulicidae, and Pygiopsyllidae are all monophyletic, while Ctenophthalmidae is paraphyletic. we support the view of some authors that revising the catchall group Ctenophthalmidae and elevating each of its constituent subfamilies to family status. [ABSTRACT FROM AUTHOR]