Despite their conserved role during chromosome segregation, centromeres are paradoxically diverse between species. Whether this reflects maintenance of diverged centromeres partitioned during speciation, or rapid intraspecies change is unknown. To understand centromere evolution, we analyzed the centromeres of 66 diverse Arabidopsis thaliana genomes, 48 of which are deposited in this Study. Therefore, this project collects the genomic PacBio HiFi reads and the corresponding de novo genome assemblies of 48 Arabidopsis thaliana natural strains. Fifteen, two and one more genome assemblies part of the Arabidopsis Pancentromere project can be found in the in the ENA database under Study Accessions PRJEB55632 (ERA17524869), PRJEB50694 (ERP135313) and PRJEB50917 (ERP135516).