Here, we generated a near telomere-to-telomere level genome assembly of marigold based on highly accurate high-fidelity (HiFi) long reads and Hi-C sequencing data. Compared to the previously reported marigold genome, the current assembly had obviously higher contiguity and higher completeness of gene set. The current genome assembly has a 27-fold increase in contig N50 size, a 12.1% increase in chromosome anchoring rate, and a 9.0% increase in BUSCO complete rate for the gene set. Besides, the current assembly has much fewer assembly errors. Based on this high-quality genome assembly, we found that the 170-bp repeats are the most abundant centromeric unit and all centromeric regions are distributed along the whole chromosomes for all 12 centromeres, indicating the existence of the holocentromeres in marigold. In addition, we analyzed the structure and phylogenetic relationship of the four PSYgenes, and revealed that these genes have diversified and possibly executed different functions in various tissues.