Four Gram-stain-negative, catalase-positive, rod-shaped and motile strains (FT55W^T, FT93W^T, CY13W^T and DS3^T) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences indicated that strains FT55W^T, FT93W^T and CY13W^T take strain Pseudoduganella danionis E3/2^T, and strain DS3^T takes strain Pseudoduganella eburnea 10R5-21^T as their closest neighbour, respectively. The genome sizes of strains FT55W^T, FT93W^T, CY13W^T and DS3^T were 6.15, 5.10, 5.31 and 5.72 Mbp with G+C contents of 61.7, 60.9, 60.6 and 64.0%, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strain FT55W^T clusters closely with Duganella radicis KCTC 22382^T and Duganella sacchari Sac-22^T, strains FT93W^T and CY13W^T form a distinct clade with P. danionis DSM 103461^T and this clade clusters with the clades of genus Duganella together, and strain DS3^T forms a distinct clade with P. eburnea JCM 31587^T and Pseudoduganella violaceinigra DSM 15887^T and this clade clusters closely with the clades of genus Massilia, respectively. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization (DDH) values among strains FT55W^T, FT93W^T, CY13W^T, DS3^T and related strains were in the ranges of 75.6–94.2% and 20.6–56.2%, respectively. Q-8 was the sole respiratory quinone of these four strains. The major fatty acids were C_16:1ω7c, C_16:0 and C_12:0. The polar lipids included phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. Considering the similar fatty acids and polar lipids profiles of species within genus Pseudoduganella, Massilia and Duganella, there is currently no justification for assigning the species of genus Pseudoduganella into the Massilia and Duganella clades in the phylogenomic tree. It is reasonable to transfer P. violaceinigra and P. eburnea to the genus Massilia as Massilia violaceinigrum comb. nov. and Massilia eburnea comb. nov., and transfer P. danionis to the genus Duganella as Duganella danionis comb. nov. Considering phylogenomic analysis, OrthoANIu data, digital DDH data and a range of physiological and biochemical characteristics, strains FT55W^T, FT93W^T and CY13W^T should be assigned to genus Duganella, and strain DS3^T should be classified as a novel species within genus Massilia, for which the names Duganella rivus sp. nov. (type strain FT55W^T = GDMCC 1.1675^T = KACC 21467^T), Duganella fentianensis sp. nov. (type strain FT93W^T = GDMCC 1.1683^T = KACC 21475^T), Duganella qianjiadongensis sp. nov. (type strain CY13W^T = GDMCC 1.1669^T = KACC 21461^T) and Massilia guangdongensis sp. nov. (type strain DS3^T = GDMCC 1.1636^T = KACC 21312^T) are proposed.