The glycopeptide antibiotic-producing soil actinobacterium Kibdelosporangium philippinense A80407 (=ATCC 49844) was sequenced using Illumina and Nanopore sequencing methodologies, and a hybrid genome assembly was generated for this type strain, with a total predicted genome length of 12,054,556 bp, 10,953 protein-coding sequences, 79 RNAs, 298 pseudogenes, and a G+C content of 65.13%.