The Menyanthaceae is a family of aquatic flowering plants with diverse leaf and floral traits, leading to uncertainty about taxonomic, phylogenetic and evolutionary relationships within this family. In order to study the molecular evolution and phylogeny within Menyanthaceae, we sequenced the complete chloroplast (cp) genomes of six representative species from Nymphoides and the monotypic genus Menyanthes. In our study, the chloroplast genomes sizes ranged from 151,985 bp for Nymphoides coronata to 154,313 bp for Menyanthes trifoliata in length. Large Single-Copy (LSC), Small Single-Copy (SSC) and Inverted Repeat regions (IRs) portrayed normal length similar to most reported angiosperms. Menyanthaceae family chloroplast genomes possess a typical quadripartite structure, conserved in genomic structure and gene order. The size of the cp genome for the seven Menyanthaceae species consistently encoded 112–113 unique genes, including 79–80 protein-coding genes, 29 transfer RNA (tRNAs), and four ribosomal RNAs (rRNAs), 17 genes were duplicated in the inverted repeat region (IR) in both Nymphoides to 18 genes in Menyanthes respectively. Comparative analysis of the chloroplast genomes showed that Nymphoides species have lost the rpl2 intron which could be a derived feature in Nymphoides species. Phylogenetic analyses were conducted using 70 protein-coding genes in other families in order Asterales. Menyanthaceae divided into two clades with robust support. The genus Nymphoides was closely related to Menyanthes. In all studied chloroplast genomes, 30 codons had relative synonymous codon usage RSCU > 1 (higher preference), 29 codons had RSCU < 1 (low preference). The largest nucleotide diversity was found in gene ccsA in CDS region and trnK-UUU-rps16 in the IGS region. Most simple sequence repeats like in other reported angiosperms were mononucleotides ending with A/T in all cp genomes.