Abstract: Trachinotus ovatus is a fish with high oxygen consumption rate, and hypoxia can easily lead to its death. Screening for InDel molecular markers for hypoxia tolerance traits in T. ovatus and discovering functional genes affecting hypoxia tolerance traits can provide guidances for selecting and breeding T. ovatus with strong hypoxia tolerance. In this study, we applied the whole genome resequencing technology to analyze the InDel differences of T. ovatus gene, excavated the InDel sites that were significantly associated with hypoxia tolerance traits in T. ovatus, and explored the candidate genes related to hypoxia tolerance traits. Altogether 693.48 Gb was obtained by sequencing, and the average value of Q30 was 90.8%. A total of 2 574 178 InDel markers were found by annotation analysis. A total of 249 395 InDel markers were found in the 50 individuals in the tolerance group, of which 2 209 were located in exons. It is found that there were mutated genes in the nucleotide excise repair signaling pathway and cell adhesion molecules. Three InDel markers (InDel 22883061, InDel 24919481 and InDel 14451779) were found to be close to the significance threshold by association analysis between InDel markers and hypoxia tolerance trait. Nine candidate genes were obtained by annotation analysis. The selected InDel markers were of great value for selecting and identifying molecular marker selection breeding. The annotated candidate genes provide a basis and references for the study of the hypoxia tolerance mechanism of T. ovatus.