The Asian green mussel Perna viridis is expanding across coastal systems of the Americas, creating demand for curated molecular references to support biosecurity, aquaculture monitoring, and comparative invasion studies. Here, we report the first complete mitochondrial genomes of invasive P. viridis from Brazil and the southwestern Atlantic, generated from two specimens collected in Santa Catarina, currently the southernmost documented sector of the Brazilian range. Long-range PCR, Oxford Nanopore sequencing, read-supported assembly, manual annotation, comparative mitogenomics, nucleotide-diversity analysis, protein-level divergence, and phylogenomic inference were used to generate and evaluate complete mitochondrial references. The two circular assemblies were 16,015 bp and 16,011 bp and contained 38 annotated features, including 13 protein-coding genes, 23 tRNAs, and two rRNAs, all on the H strand, with an identical A+T content of 67.5%. Pairwise comparisons among the four complete P. viridis mitogenomes analyzed showed high overall similarity but retained 20–125 SNPs/mismatches and one to 12 indel events. Gene order was conserved within P. viridis but differed from P. canaliculus and P. perna, and phylogenomics placed the Brazilian assemblies within the P. viridis clade. These curated mitogenomes provide initial complete mitochondrial references for future marker testing and comparative studies of P. viridis in the southwestern Atlantic, but the two-specimen dataset should not be used to infer population origin, invasion routes, or connectivity.

The Asian green mussel Perna viridis is expanding across coastal systems of the Americas, creating demand for curated molecular references to support biosecurity, aquaculture monitoring, and comparative invasion studies. Here, we report the first complete mitochondrial genomes of invasive P. viridis from Brazil and the southwestern Atlantic, generated from two specimens collected in Santa Catarina, at the current southern Brazilian invasion front. Long-range PCR, Oxford Nanopore sequencing, read-supported assembly, manual annotation, comparative mitogenomics, nucleotide-diversity analysis, protein-level divergence, and phylogenomic inference were used to generate and evaluate complete mitochondrial references. The two circular assemblies were 16,015 bp and 16,011 bp and contained 38 annotated features, including 13 protein-coding genes, 23 tRNAs, and two rRNAs, all on the H strand, with an identical A+T content of 67.5%. Pairwise comparisons among complete P. viridis mitogenomes showed high overall similarity but retained 20-125 SNPs/mismatches and one to 12 indel events. Gene order was conserved within P. viridis but differed from P. canaliculus and P. perna, and phylogenomics placed the Brazilian assemblies within the P. viridis clade. These curated mitogenomes establish a genomic baseline for molecular surveillance and future invasion-focused studies of P. viridis in the southwestern Atlantic.