Vibriosis is a major challenge in shrimp hatcheries and often associated with 100% mortality in mysis and early postlarval stages of penaeid shrimp. It is also a major pathogen of marine and brackishwater finfish culture. Vibrio harveyi has been implicated as a primary causative agent of vibriosis in shrimp hatchery. In recent times, several closely related species such as V. campbellii, V. owensii, V. jasicida, V. rotiferianus etc. have also been frequently associated with vibriosis. These species share high level sequence similarity in 16S rRNA gene and DNA-DNA homology and hence kept together as the part of Vibrio harveyi clade. V. harveyi represents the most characterized species under the harveyi clade. Several virulence factors such as chitinase, hemolysin, serineprotease, metalloprotease, quorum sensing, lysogenic bacteriophages etc. have been described as pathogenic determinants. However, the virulence of V. harveyi is still an enigma. Further, little information is available regarding the virulence of other species. Hence, to understand the virulence of harveyi clade species, a pangenome analysis comprising 60 genomes; V. harveyi (23), V. campbellii (14), V. owensii (9), V. jasicida (6), V. rotiferianus (4) and V. natriegens (4 isolates) was carried out using Roary pipeline. These genomes were further analyzed for toxins, secretion systems and quorum sensing using bioinformatic tools such as standalone BLAST and T346Hunter. The study revealed that harveyi clade has 1710 core genes (present in all isolates) against the pangenome size of 29,411 genes. Further, 23,001 genes were present in less than 15% isolates. The core gene based phylogeny revealed that the six species belonged to six separate clusters. However, six isolates of V. harveyi have been reclassified as V. campbellii (KC13.17.5), V. owensii (CUB2, 1DA3) and V. jasicida (BSW5, BSW7 and MOR3). Three parallel quorum sensing systems have been reported in V. harveyi. This includes luxM based AI-1, luxS based AI-2 and cqsA based cholera autoinducer 1. Bioinformatic analysis revealed that all the three systems were present in V. harveyi, V. campbellii, V. jasicida and V. owensii. However, luxM system was absent in V. natriegens and V. rotiferianus. Among the six types of secretion systems, the T1SS and T2SS were present in all the isolates of Harveyi clade, irrespective of species and their virulence behavior. However, the T3SS and T6SS showed species specific and T4SS strain specific pattern. Apart from these several novel effector toxins were characterized and their importance in virulence of harveyi clade species is under further investigation. The present study signified that secretion systems could be playing a significant role in deciding the virulence pattern of harveyi clade species.