Abstract Sap beetles are widely distributed in the Holarctic and tropical regions, with diverse feeding habits and strong adaptability. They play important roles in the decay of plants, the spread of fungi and bacteria, and the carbon and nitrogen cycles in agricultural ecosystems. Here, we provide an annotated, chromosome level reference genome assembly for a sap beetle Glischrochilus (Librodor) japonius (Motschulsky, 1857), a member of the family Nitidulidae, assembled using PacBio HiFi and Hi-C data from female specimens. The final assembly has a total size of 789.06 Mb, with 94.91% of the sequence successfully anchored to 10 chromosomes. The scaffold N50 is 77.84 Mb, and BUSCO (endopterygota_odb10 database) completeness is 97.20%. Repetitive elements comprise 54.67% of the genome (431.38 Mb). We identified 1,673 noncoding RNAs and predicted 22,526 protein-coding genes in the genome. This genome will serve as a valuable resource for advancing our understanding of the evolution and ecology of sap beetles, and will facilitate comparative studies of genome structure within the Nitidulidae family.