Pseudomonas genus has the largest number of species among bacterial genera. Scientists have divided Pseudomonas genus to different groups. Today, this genus has been divided to two linages, 10 groups and 9 subgroups. One of the most important groups of this genus is P. putida group. So far, 17 species have been described in this group. The isolates of this group have different potentials, some of them are bioremediation, some of them are plant beneficial bacteria (included plant growth promoting bacteria (PGPB) and antagonist) and some of them are clinical. In this research, the abilities of 12 Iranian isolates belong to P. putida group were investigated by using phylogeny tree. This isolates were obtained from collection of plant protection group of Khuzestan Agriculture Sciences and Natural Resources University. First, the phylogeny tree was drown by concatenating of 3 housekeeping genes rpoD, gyrB and rrS. A total of 58 isolates including,12 Iranian isolates, 17 type strains and 29 proposed isolates were used for constructing phylogeny tree. Phylogeny tree showed 11 clusters. Traits of 46 isolates (17 type strains and 29 proposed isolates) were obtained from the corresponding literatures. Investigation of phylogeny tree and functional attributes showed that isolates in clusters 1, 4 and 11 had bioremediation characteristics. Isolates in clusters 3, 6 and 10 were antagonist. Isolates in clusters 2, 7 and 9 clusters were included bioremediation and plant beneficial bacteria. Isolates in clusters 5 and 8 had clinical and bioremediation features. Clustering of isolates with similar characteristics in a cluster showed that regarding the source of isolates and phylogeny tree the ability of isolates are predictable. Iranian isolates placed in 4 clusters, 3, 9, 10, 11. The antagonistic trait of six isolates had been shown and they were in clusters 3, 9 and 10. The six more isolates were not antagonist and the feature of these isolates was not clear. These isolates placed in clusters 9 and 11. Regarding the source of these isolates and characteristics of other isolates of these clusters, plant growth promoting traits is predictable for these isolates. This isolates may have bioremediation aspects too.