Melothria scabra
has gradually become an economically important plant worldwide. The complete chloroplast genome of
M. scabra
has a length of 156,744 bp, contains a large single-copy (LSC) region (86,387 bp), a small single-copy (SSC) region (18,055 bp), and two inverted repeats (IRs) with the same length of 26,151 bp. In total, 126 genes were detected, including 83 protein-encoding genes, 35 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For phylogenetic analysis,
M. scabra
has a closer genetic relationship with
Cucumis sativus
and
Citrullus lanatus
. The complete chloroplast genome sequence of
M. scabra
would promote the germplasm exploration, phylogenetic relationships, and molecular biology researches in
Melothria
.