Malaria causes >600 thousand fatalities each year, with most cases attributed to the human-infectiousPlasmodium falciparumspecies. Many rodent-infectiousPlasmodiumspecies, likePlasmodium bergheiandPlasmodium yoelii,have been used as model species that can expedite studies of this pathogen.P. yoeliiis an especially good model for investigating the mosquito and liver stages of development because key attributes closely resemble those ofP. falciparum. Because of its importance, in 2002 the 17XNL strain ofP. yoeliiwas the first rodent malaria parasite to be sequenced. Although this was a breakthrough effort, the assembly consisted of >5000 contiguous sequences that adversely impacted the annotated gene models. While other rodent malaria parasite genomes have been sequenced and annotated since then, including the relatedP. yoelii17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become thede factoreference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly forP. yoelii17XNL using PacBio DNA sequencing. In addition, we use Nanopore and Illumina RNA sequencing of mixed blood stages to create complete gene models that include coding sequences, alternate isoforms, and UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic framework for studies with this commonly used rodent malaria model species.