| Summary: | The plant mitochondria play a crucial role in various cellular energy synthesis and conversion processes and are essential for plant growth. Watercress (<i>Oenanthe javanica</i>) is a fast-growing vegetable with strong adaptability and wide cultivation range, and it possesses high nutritional value. In our study, we assembled the <i>O. javanica</i> mitochondrial genome using the Illumina and Nanopore sequencing platforms. The results revealed that the mitochondrial genome map of watercress has a circular structure of 384,074 bp, containing 28 tRNA genes, 3 rRNA genes, and 34 protein-coding genes. A total of 87 SSR (simple sequence repeat) loci were detected, with 99% composed of palindrome repeats and forward repeats, while no complementary repeats were identified. Codon preference analysis indicated that watercress prefers to use codons encoding leucine, isoleucine, and serine with a preference for A/U-ending codons. Phylogenetic analysis showed that watercress is closely related to species of <i>Bupleurum</i>, <i>Apium</i>, <i>Angelica</i>, and <i>Daucus</i>, with the closest evolutionary relationship observed with <i>Saposhnikovia divaricata</i> and <i>Apium graveolens</i>. This study provides a valuable resource for the study of the evolution and molecular breeding of watercress.
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