<p>The development of insertion‒deletion (InDel) markers provides a valuable tool for genetic and genomic studies in tea (<i>Camellia sinensis</i>) plants. In this study, 4,370,229 InDel markers were identified through genome resequencing of Lingtou Dancong (BY) and Shuixian 7 (SX7). Transcriptome based on RNA sequencing revealed differential expression of 1,125 genes involved in plant-pathogen interaction pathways. Based on genome resequencing of the two tea varieties with a shared genetic background and RNA-seq dataset for post-anthracnose infection, molecular markers for anthracnose resistance in tea plants were developed by identifying specific InDels within the disease resistance-associated interval. The InDel marker linked to anthracnose resistance was located at 123,508,930&#xa0;bp on chromosome Chr10. Tea plants with DNA bands of 590-bp or heterozygous bands amplified by the primer were resistant to the disease, while those with 431-bp bands were susceptible. When tested across 206 different tea varieties, the Indel marker CsRc demonstrated an 88.59% genotype–phenotype match, confirming its applicability for detecting anthracnose resistance/susceptibility in tea plants. Additionally, the CsRc marker was found to be located within the serine/threonine protein kinase gene, suggesting that ATP plays a critical role in the metabolic processes of tea plants. Taken together, our findings unravel important Indel markers for efficiently distinguishing valuable tea genotpes with desirable resistance to anthracnose, which holds great potential for facilitating disease resistance breeding in the future.</p> Graphical Abstract <p></p>