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The nanomachine referred to as the type III secretion system (T3SS) is used by many Gram-negative pathogens or symbionts to inject their effector proteins into host cells to promote their infections or symbioses. Among the genera possessing T3SS is <i>Vibrio</i>, which consists of diverse species of Gammaproteobacteria including human pathogenic species and inhabits aquatic environments. We describe the genetic overview of the T3SS gene clusters in <i>Vibrio</i> through a phylogenetic analysis from 48 bacterial strains and a gene order analysis of the two previously known categories in <i>Vibrio</i> (T3SS1 and T3SS2). Through this analysis we identified a new T3SS category (named T3SS3) that shares similar core and related proteins (effectors, translocons, and chaperones) with the Ssa-Esc family of T3SSs in <i>Salmonella</i>, <i>Shewanella</i>, and <i>Sodalis</i>. The high similarity between T3SS3 and the Ssa-Esc family suggests a possibility of genetic exchange among marine bacteria with similar habitats.