【Objective】 This study reported the complete genome sequence of Elsinoë murrayae and comparisons with the Elsinoë australis poplar spot anthracnose (PSA) pathotype, aiming to provide a reference for explaining the pathogenic and specialized mechanism of E. murrayae. 【Method】 A draft genome sequence of E. murrayae was sequenced to annotate protein-coding genes and carbohydrate-active enzyme genes. Small secreted protein genes and secondary metabolite biosynthetic gene clusters were screened. According to the orthologous relationship of the genes of Elsinoë spp., the common specific genes of E. murrayae and E. australis (PSA) were identified, and the differential genes between E. murrayae and E. australis (PSA) were screened out and analyzed using GO enrichment. The mating type locus was identified, and the mating type of isolates was detected using PCR with specific primers. 【Result】 A 20.7 Mb genome with 99% completeness was obtained. A total of 8 256 protein-coding genes were predicted, including 486 carbohydrate-active enzyme genes, 193 small secreted protein genes, and 16 secondary metabolite biosynthetic gene clusters (GenBank accession No.: NKHZ00000000). The phylogenetic analysis and whole genome synteny comparisons showed that E. murrayae and E. australis (PSA) had the closest relationship, and the two fungi had 12 common specific genes which were not found in other Elsinoë spp. Compared with the two fungi, 752 and 1 746 different genes were screened, of which encoding proteins were mainly involved in carbohydrate metabolic processes and toxin metabolic processes. The mating type of all the isolates was MAT1-2. 【Conclusion】 The genome of E. murrayae, a fungal pathogen of willow, was reported for the first time. The candidate genes responsible for the host specialization were screened, and the mating system of E. murrayae was analyzed. These studies provided key information for willow disease control and willow-pathogen interaction.