We present the genome sequence of Leishmania mexicana MNYC/BZ/62/M379 modified to express Cas9 and T7 RNA-polymerase, revealing high similarity reference (MHOM/GT2001/U1103). Through RNAseq-based annotation coding sequences untranslated regions, we provide primer for construct sgRNA template generation CRISPR-assisted gene deletion endogenous tagging.