Tunicates or Ascidian (sea squirt) is a very diverse and cosmopolitan organism, also could live in contaminated environment. Tunicates could harbor various associative bacteria that could produce potential secondary metabolites and adapt to heavy metals. This research aimed to isolate and characterize associative bacteria of Phallusia sp. (Ascidian) using Sea Water Complete Agar (SWCA) media with Pb heavy metals addition. Associative bacteria were isolated from different parts of Phallusia sp. body tissue (basal, middle, and apical part), using several concentrations of Pb added to the media. Three different concentration was applied, K-as control (non-added Pb), K+ (0.008 mgL-1 Pb), and P (0.05 mgL-1 Pb). Result showed that total count of associative bacteria from different parts of body tissue was not significantly different, in neither of Pb concentrations (ANOVA, P value of 0.16). There were 24 isolates with different colonies successively found from all media. Most of the isolate’s colony has white pigmentation, dominated by Gram-negative bacteria. Motility assay showed that all bacteria isolate was motile, with 16 isolates could hydrolyse starch. Lipase activity was found in 20 isolates, and all isolates have catalase, and glucose and mannose fermentative activity. There were 21 isolates with cytochrome oxidation activity. Morphological and physiological characterization suggest that associative bacteria belonged to five groups of bacteria, including four different genera (Alteromonas, Bacillus, Deleya, and Vibrio). Kruskal-Wallis test result showed that the genus composition between each Pb concentration was insignificantly different, with a P value of 0.878.