Leiognathid fish and cephalopod grouped under the family Loliginidae and Sepiolidae are known to harbour luminescence bacterial symbionts in their light emitting organs. Association of bacteria and squid have been well studied in few species of squids mostly in the American subcontinent and in Japan coast. However, there are very few reports of such association from Indian subcontinent. In this study we have screened 15 samples consisting of 6 each samples of Uroteuthis duvauceli and toothed pony fish Gazza minuta, 3 samples of Sepioteuthis lessioniana from 5 different locations in Mumbai, Ratnagiriand Tamilnadu. PCR-RFLP, lux gene amplifications and 16SrRNA analysis revealed that all of the 348 luminescent bacteria isolated from the light organs of squid and pony fishes were identified as Photobacterium leiognathi whereas all the isolates from sea water comprised of Vibrio harveyi. Earlier reports indicates host-symbiont association is very specific and restricted with one symbiotic species specific to the host, whereas in the Indian subcontinent, squid and leiognathid fish from different locations, distributed as far as 2000 km were found to harbour only a single symbiont P. leiognathi irrespective of its sampling location or season, proving that the specificity is related to geographic distribution. Specificity of the host symbionts is also possibly related to the availability of the beneficial microbes in the vicinity. In the Indian subcontinent V. harveyi and P. leiognathi are the dominant luminescence microflora in the marine environment of which V. harveyi is a potent pathogen to invertebrates and can survive under strong light condition in the coastal area whereas P. leiognathi is sensitive to light and mostly involved in symbiosis.