Abstract
Cynometra cebuensis F. Seid., a critically endangered species endemic to Cebu, Philippines, lacks published genomic data. We present its first complete chloroplast genome, assembled using Illumina paired-end sequencing. The 158,474 bp genome includes a large single-copy (86,821 bp), small single-copy (19,329 bp), and two inverted repeats (26,162 bp each), with a GC content of 36.4%. It contains 125 genes: 80 protein-coding, 37 tRNA, and eight rRNA. Phylogenetic analysis places C. cebuensis in a monophyletic group within Detarioideae, closely related to C. lenticellata, providing essential data for its identification, phylogeny, and conservation.