Scirpus × mariqueter (Tang & F.T.Wang) Tatanov, which is endemic to eastern estuaries in China, is a tidal zone-engineering species with great promise for managing greenhouse gases and enhancing ecosystem resilience against invasive species. Although S. mariqueter is widely recognized as a hybrid species derived from Bolboschoenus planiculmis (F. Schmidt) T.V. Egorova and Schoenoplectus triqueter (L.) Palla, its speciation remains highly controversial. The lack of a reference genome is the major cause of this ambiguity. We generated the first chromosome-level genome assembly for S. mariqueter combining PacBio long-reads, Illumina short-reads, and the Hi-C method. The genome assembly consisted of 227.75 Mb (contig N50: 3.89 Mb). We also constructed a haploid karyotype comprising 54 pseudochromosomes. The average size of these pseudochromosomes was small (4.05 Mb). Thirty-two pseudochromosomes were assembled to a telomere to telomere level. Repetitive elements represented approximately 54.12% of the genome. We predicted and annotated 25,239 protein-coding genes. The overall BUSCO score was 95.10%, with notably few duplicated genes (1.70%). This high-quality genome provides critical data for future studies.