Background <p>The sea aster, <i>Tripolium pannonicum</i> (Jacq.) Dobrocz 1962, the sole species of the genus <i>Tripolium</i>, is an annual halophyte. Native to estuarine and coastal marsh ecosystems, it plays a vital ecological role in maintaining the stability of saline habitats and supports biodiversity. In addition, it holds significant economic value as a biomass resource. Despite its ecological and economic importance, genomic data for <i>T. pannonicum</i> have been lacking. Here, we report the first complete chloroplast genome of <i>T. pannonicum</i>, providing a foundational resource for phylogenetic and ecological studies of halophytic species within the Asteraceae family.</p> Results <p>The assembled chloroplast genome has a total length of 153,075&#xa0;bp and a GC content of 37.2%. It comprises four distinct subregions: a large single copy (LSC) region of 84,385&#xa0;bp, a small single copy (SSC) region of 18,028&#xa0;bp, and two inverted repeats (IRs) of 25,331&#xa0;bp each. The chloroplast genome encodes 127 genes, including 88 protein-coding genes (PCGs), 34 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenomic analysis using the whole PCGs revealed that the chloroplast genome of <i>T. pannonicum</i> is closely related to members of the genus Aster.</p> Conclusions <p>This study provides the first chloroplast genome for the genus <i>Tripolium</i>, addressing a significant gap in genomic data for halophytic members of the Asteraceae. The results enhance our understanding of the phylogenetic placement and evolutionary relationships of <i>T. pannonicum</i> within the tribe Astereae. Beyond taxonomy, the chloroplast genome offers a molecular foundation for species identification, biogeographic research, and the genomic approach for the estimation of population structure. These data are especially relevant in providing molecular tools that can be applied to ecological monitoring and conservation strategies for salt-tolerant plant species threatened by habitat degradation and climate change.</p>