Vibrio harveyi is a pathogen of various aquatic organisms that has been recently associated with massive mortality episodes in the aquaculture industry. Recurrent outbreaks of vibriosis are closely correlated with the capacity of this bacterial species to survive long-term starvation conditions. To study the regulation mechanism of gene expression at the transcriptional level in V. harveyi under starvation conditions, the transcriptomic response profiles were determined of the Portunus trituberculatus pathogen V . harveyi strain DY1 under normal conditions and after four weeks of starvation. A total of 4679 and 4661 genes were expressed in the non-starved and starved cells, respectively. The significantly differentially expressed genes (DEGs) between non-starved and starved groups were identified, in which 255 genes were up-regulated and 411 genes were down-regulated. GO analysis and KEGG enrichment analysis were used to analyze the DEGs and revealed the involvement of these DEGs in many pathways, including ABC transporters, flagellum assembly, and fatty acid metabolism. Several DEGs were randomly selected and their expression levels were confirmed by quantitative real-time PCR (qRT-PCR). This is the first comprehensive transcriptomic analysis of starvation effects in V . harveyi . Our findings will facilitate future study on stress adaptation and survival mechanisms of V . harveyi .