Black spot needle blight is a serious conifer disease ofPinus sylvestrisvar.mongolicaoccurring in Northeast China, which is usually caused by the plant pathogenic fungusPestalotiopsis neglecta. From the diseased pine needles collected in Honghuaerji, theP. neglectastrain YJ-3 was isolated and identified as the phytopathogen, and its culture characteristics were studied. Then, we generated a highly contiguous 48.36-Mbp genome assembly (N50 = 6.62 Mbp) of theP. neglectastrain YJ-3 by combining the PacBio RS II Single Molecule Real Time (SMRT) and Illumina HiSeq X Ten sequencing platforms. The results showed that a total of 13,667 protein-coding genes were predicted and annotated using multiple bioinformatics databases. The genome assembly and annotation resource reported here will be useful for the study of fungal infection mechanisms and pathogen–host interaction.