Recently, integron gene cassette metagenome has been discovered as a class of mobile DNA elements that play a role in the functional genome of marine bacteria. This importance of integron was extended from the original idea that integron is the main key for evolution and adaptation of pathogenic bacteria against antibiotic attacks. In this review, we highlighted on the diversity, function and applications of integron/gene cassette metagenome in marine environments. Each environment has specific selective characteristics that could shape the integron gene cassette metagenome, to be an environment adaptive DNA tool. This idea led us to innovate synthetic integrons with wide biotechnological applications.