Abstract: To investigate the phylogeny of Juncaginaceae and enrich its genetic resources, the complete chloroplast genomes of Triglochin maritima and Triglochin palustris were sequenced, assembled, annotated, and characterized. In addition, the phylogenetic relationships of Juncaginaceae and closely related taxa were reconstructed. The results indicate that the chloroplast genomes of Triglochin maritima and Triglochin palustris exhibit circular structure with lengths of 155881 and 155803 bp, respectively, containing 57 and 60 SSRs and all 49 long repetitive sequences. In addition, Both genomes also show a preference for codons ending in A/U. Phylogenetic analysis shows that these two Juncaginaceae species form a single branch with a significant genetic distance from closely related taxa, diverging from Potamogeton, Phyllospadix, Zostera, Halodule, Syringodium, and Ruppia approximately 78.67 million years ago. In conjunction with the distributional habitat differences, this study supports the elevation of Triglochin to family status within Juncaginaceae. This study provides a theoretical foundation for investigating chloroplast genome structure evolution of Juncaginaceae and offers valuable insights for species conservation and scientific utilization of Juncaginaceae and its related taxa.