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Phalaenopsis malipoensis Z.J. Liu et S.C. Chen, 2005 is a valuable species of Orchidaceae with significant ornamental value. This study reports the first complete chloroplast genome of P.malipoensis was collected integrally and clarified further. The genome was 144,528 bp in length and comprised four regions, including a pair of inverted repeats each 24,710 bp, a large single-copy region of 83,475 bp, and a small single-copy region of 11,633 bp. The whole genome contained 125 genes, including 8 rRNAs, and 39 tRNAs. Phylogenetic analysis indicated that P. malipoensis was closely related to Phalaenopsis lobbii. The analysis of P. malipoensis chloroplast genome will provide significant data for the identification and further improvement of P. malipoensis.

Cymbidium hookerianum Rchb.f. is an ornamental orchid with large flowers and delicate aroma. Here, we reported the complete chloroplast genome sequence of C. hookerianum. The total chloroplast genome cycle was 155,447 bp. It displayed a typical structure including one large single-copy (LSC, 84,186 bp) region, one small single-copy (SSC, 17,839 bp) region, and two inverted repeat (IRs, 26,711 bp). 124 genes (78 CDSs, 38 tRNAs, 8 rRNAs) were encoded by the cp genome. The average GC content of this sequence was 36.8%. The phylogenetic analysis revealed C. hookerianum and C. changningense are sisters. The groundwork of chloroplast genome would provide available reference for molecular taxonomy and breeding.

An important horticultural moth orchid in China, Phalaenopsis lobbii, has small and lovely flowers with unique labial characteristics. We sequenced the chloroplast genome (cpDNAs) of P. lobbii and analyzed the structural characteristics of its complete cpDNAs sequence. The results showed that P. lobbii had a typical circular double-stranded tetrad structure with the average GC content of 36.60%, and its total length was 144,607 bp. The complete chloroplast was annotated with 125 genes, eight rRNAs and 38 tRNAs. Phylogenetic tree displayed that P. lobbii was closely related to P. equestris, P. aphrodite subsp. formosana, P. ‘Tiny Star’ and P. japonica. This published cpDNAs of P. lobbii will provide information for future phylogenetic and artificial breeding of Phalaenopsis.

Phalaenopsis mannii, one of the native Phalaenopsis in China, is an important parent for breeding new varieties. However, its position has been unclear in Phalaenopsis. The obtained high-quality P. mannii chloroplast genome will provide useful information for phylogenetic and future breeding of Phalaenopsis. Herein, we reported a complete chloroplast genome of P. mannii from Yunnan, China. The sequencing data obtained from BGISEQ-500 platform were assembled. This sequence had a circular molecular length of 148,596 bp and contained a total of 127 genes with an average GC content of 36.7%. Phylogenetic analysis indicated that Phalaenopsis was monophyletic with strong support, in which the P.mannii was the sister-group of Phalaenopsis aphrodite subsp. formosas, Phalaenopsis ‘TinyStar’ and Phalaenopsis equestris.

Cymbidium maguanense is a valuable orchid endemic to China, with delicate smelling, ivory white flower, and showy yellow labellum. Herein, we reported the complete chloroplast genome of C. maguanense. This chloroplast genome was 156,530 bp in length. It presented a typical structure including a large single-copy region (LSC, 85,112 bp), a small single-copy region (SSC, 17,874 bp), and two inverted repeat regions (IRs, 26,772 bp). It contained 138 genes, 37 tRNA, and 8 rRNA with an average GC content of 36.8%. Besides, the phylogenetic analysis showed that C. maguanense displayed a closer kinship to C. eburneum in the section Eburnea under subgenus Cymbidium. This chloroplast genome will provide a reference for future studies on species evolution, germplasm resources utilization, and genetic engineering of genus Cymbidium.