Lagenaria Ser. is one of the genera of Cucurbitaceae Juss., nom. cons. comprising of economically important crops. So far only the chloroplast genome (cp genome) of Lagenaria siceraria var. microcarpa (Naudin) H. Hara has been reported in Lagenaria. However, there is no molecular data and analysis of the cp genome of Lagenaria abyssinica (Hook.f.) C.Jeffrey. Here, we assembled and annotated the whole cp genome of L. abyssinica and explored the relationship of the taxon to which it belongs with other taxa. The cp genome of L. abyssinica (156,800 bp) comprised of large and small single-copy (LSC, SSC) regions of sizes 86,478 bp and 17,992 bp respectively, and two identical inverted repeat regions of size 26,165 bp. The cp sequence contained 132 genes, which were composed of protein-coding genes (87), transfer RNA (37) genes, and ribosomal RNA (8) genes. Chloroplast genomes in Cucurbitaceae did not differ much in structure, gene order, the content of base pairs (GC%), and codon usage. There were 20 highly variable loci and 32 positively selected genes. Phylogenetic trees showed that Lagenaria was the sister clade of Citrullus Schrad., both of which in turn form a greater clade with Benincasa Savi and Zehneria Endl. Lageanria Ser. was a member of the Benincaseae Ser., which shared a close phylogenetic relationship with Cucurbiteae Juss., and some new insights have been gained about other inter-clade relationships. The cp genome of L. abyssinica is an important molecular resource for the classification and divergence time of this genus and family Cucurbitaceae. This study enriched the genomics data of Cucurbitaceae and contributes to the further development of DNA barcoding and molecular labeling research.