The InDel markers have been extensively used in molecular marker-assisted breeding for fruit trees. However， limited studies have been conducted on their application in Chinese bayberry （Morella rubra）， a traditional Chinese fruit tree. This study identified 25831 InDels， ranging from 1 to 50 bp in size， through whole-genome resequencing and bioinformatics analysis of 103 Chinese bayberry core germplasm accessions. The frequency of InDel variation across different chromosomes ranged from 1/11297 to 1/8903， with chromosome CM025856.1 exhibiting the highese frequency of InDel mutation. Annotation analysis showed that 1312 InDels were located in gene exon regions， while 21055 and 6659 InDels were distributed in the intergenic and intron regions， respectively. Gene Ontology （GO） analysis indicated that these InDels were primarily associated with for cellular processes and metabolic processes in biological processes， and with binding and catalytic activity in molecular functions. KEGG pathway analysis demonstrated that the InDel-containing genes were predominantly involved in secondary metabolism， carbon metabolism and nucleocytoplasmic transport. Genome-wide association analysis identified 20 InDels significantly associated with fruit maturity traits. Functional annotations of these InDels revealed associations with mitochondrial and plastid structural genes， riboside triphosphate hydrolase， and cytokinin signaling proteins. Further validation and analysis identified the InDel EP-18 marker as having the highest accuracy （89.25%） for identifying fruit maturity traits. Gene prediction analysis indicated that this locus encodes an early nodulin family gene. In conclusion， the InDel EP-18 marker identified in this study provides an important theoretical basis for molecular assisted breeding of Chinese bayberry.