Eucheumatoid seaweeds are highly valued globally for their carrageenan. Members of this group are widely distributed and cultivated throughout the Indo-Pacific. Despite various molecular studies on this group, mitogenome research in eucheumatoids has only recently explored a limited number of species, leaving overall diversity largely unexplored. In this study, 26 complete mitogenomes of eucheumatoids from the Indo-Pacific were sequenced, including the first complete sequences for wild genotypes of Eucheuma platycladum, Kappaphycus striatus, Kappaphycopsis cottonii, and an unidentified species of Kappaphycus from Africa. The eucheumatoid mitogenomes range from 25.1 to 25.5 kb in size, containing 50 genes (24 protein-coding genes, 24 tRNA genes, two rRNA genes, and a single intron) bearing extensive gene synteny across species. Phylogenetic analyses using concatenated mitochondrial genes recovered strong clades for each group, with the exception of the genus Eucheuma. Apart from atp9, gene marker evaluations showed that all genes could be used for species identification. The utility of four genes, atp4, nad3, nad4, and nad6, was found to be effective for resolving intergeneric relationships. These findings provide a foundation for comparative analysis useful for resolving phylogenetic relationships and outstanding taxonomic issues, cultivar development, and conservation efforts. Expanding species coverage and incorporating plastome analyses would contribute to a more complete understanding of the genomic diversity and evolutionary history of this economically important group of seaweeds.