Rock lobster Panulirus homarus is a commercially important species exploited in India and abroad, and has proven mariculture potential. The present study was focused on isolation, screening, biochemical and molecular level characterization of putative probiotic bacteria from the intestine of P. homarus sampled along the south west coat of India. The total plate count in the intestine ranged from 8 ×104 to 3.8 × 106 cfu g-1 (colony forming unit per g tissue). The intestinal bacterial flora as identified by the physiological and biochemical characters, consisted of strains belonging to Enterobactericeae, Bacillaceae, Vibrionaceae, Pseudomonadaceae, Micrococcaceae and Moraxellaceae families. Among these, four strains which were functionally diverse viz. pigmented, proteolytic and denitrifying strains were characterized by molecular methods following 16S rDNA sequencing and were identified as Bacillus aerophilus KU296018, Micrococcus aloeverae KU296019, Psychrobacter sanguinins KU296021 and Pseudomonas caeni KU296020. In aquaculture beneficial bacteria could be introduced into artificial diets. The enzyme producing microorganisms isolated from the crustacean digestive tracts in the present study may be beneficially used as a probiotic supplement while formulating the diet, especially in the larval stages
