MADS-box genes are transcription factors that control eukaryote development and growth, particularly in regulating flower development in plants through the ABC(D)E model. Revealing the functions of MADS-box genes and their regulatory network, together with other related genes, will play a key role in understanding the evolution of angiosperms. However, studies on floral MADS-box genes in many major lineages of angiosperms have not yet been conducted. Carex, with approximately 2,000 species, is the fifth largest genus in angiosperms and has unique floral morphology, including the perigynium, a sac-like structure covering gynoecium. Detection of MADS-box genes and their functional studies in Poales have primarily focused on Poaceae, which includes several model plants, rather than Cyperaceae. In this study, we detected MADS-box genes in Carex as a representative of Cyperaceae. We first determined draft genomes from five Carex species (C. siderosticta, C. paxii, C. dickinsii, C. breviculmis, and C. capricornis) based on both long-read (Nanopore) and short-read (Illumina and MGI) sequences. The genomes were of high quality, with 48 to 168 contigs, and had BUSCO values over 94.5%. We analyzed three previously reported Carex genomes and representatives of other Poales lineages, in conjunction with five newly sequenced genomes from this study. The MADS-box genes from Amborella trichopoda, Oryza sativa, and Arabidopsis thaliana were used as references in the detection process. The maximum-likelihood tree using amino-acid aligned DNA matrix showed unique duplication and deletion events in the evolutionary history of MADS-box genes in Carex. We produced transcriptomes of each floral organ from two representative species and compared them with those in Arabidopsis and rice. We also compared various methods for detecting MADS-box genes and discussed the boundary of the MADS-box gene family. Our findings will shed light on the floral structure evolution and genome evolution of Carex, which serves as a representative for the Cyperaceae.