Lasiodiplodia theobromae is a pathogenic fungus associated with tropical perennial fruit plants worldwide. In apple trees, L. theobromae causes dieback and canker, a disease that affects the architecture of the wood producing the progressive death of branches and stems, from the tips to the base, invading the vascular tissue, manifesting necrotic lesions in the bark, impeding the flow of nutrients and water. The present work reports the whole genome de novo sequencing (WGS) of L. theobromae strain Bot-2018-LT45 isolated from apple trees with dieback symptoms. Genomic DNA of L. theobromae was sequenced using Illumina paired-end short-read technology (NovaSeq6000) and PacBio SMRTbellTM (Single Molecule, Real-Time) long-read technology. The genome size was 44.17 Mb. Then, assembly and annotation revealed a total of 12,948 genes of which 11,634 encoded proteins. The genome was assembled into 34 contigs with an N50 (Mb) value of 3.23. This study is the first report of the L. theobromae genome de novo obtained from apple trees with dieback and canker symptoms in the Maule Region, Chile. This genetic information may set the basis for future study of the mechanisms of L. theobromae and establish the possibility of specific molecular improvements for the control of dieback and canker.