Numerical phenetic analysis was used to compare phenotypic data obtained from 6 isolates of pigmented bacteria strains taken from marine and river aquatic. Each strain was tested for 120 characters, analysed using the simple matching (SSM) and Jaccard (SJ) similarity indices with unweighted pair-group method with arithmetic mean (UPGMA) clustering method. All of the strains classified into two clusters, cluster A as marine pigmented bacteria and cluster B as river pigmented bacteria. Differences were observed between the dendrograms derived from the SSM and SJ. Presence of bacteriochlorophyll-a (Bchl-a), carotenoids, as well as other biochemical tests of three marine pigmented strains were in match with key characters of the genera Roseobacter, Roseateles and Erythrobacter. Three of river pigmented strains were identified as Xanthobacter, Flavobacterium and Pseudomonas. It was proved that the marine and river pigmented bacteria isolates showed a relative phenotypically distance. It was clearly seen that the phenetic approach was a necessary tool to delimitate and identify the pigmented bacteria from different habitats.