Here we present reference genomes for the Plasmodium cynomolgi Berok and Ceylon strains generated with Oxford Nanopore (ONT) and Illumina reads. P. cynomolgi is a parasite of old-world monkeys and serves as an important model for P. vivax. The asexual blood stages of P. cynomolgi Berok have been adapted to long-term culture and are increasingly being used to study vivax-type biology.