The fungal genus
Neonectria
contains many phytopathogenic species currently impacting forests and fruit trees worldwide. Despite their importance, a majority of
Neonectria
spp. lack sufficient genomic resources to resolve suspected cryptic species. Here, we report draft genomes and assemblies for
Neonectria magnoliae
NRRL 64651 and
Neonectria punicea
NRRL 64653.