The region of Eastern Sabah, Malaysia, harbours a rich diversity of eucheumatoid (i.e. Kappaphycus and Eucheuma spp.) algae. The global cultivation of this group of red algae has generally been increasing over the last five decades to respond to worldwide demand in carrageenans. Yet, the industry relies on a handful of clonally propagated individuals; hence the diverse populations of eucheumatoids in Eastern Sabah, Malaysia are widely regarded as potential source of novel germplasm useful for marker-assisted breeding. Based on an unprecedented depth of sampling of previously surveyed areas, this study was undertaken to determine the specific and intraspecific diversity of wild eucheumatoids in the Eastern Sabah region. Six eucheumatoid populations were haphazardly sampled, yielding 195 specimens. Using our previously established methods, the cox2–3 spacer (332 bp) and cox1 (1,407 bp) genetic markers were sequenced and analysed. Our data confirm that eucheumatoids in this area are extremely diverse: four eucheumatoid species in total were encountered and up to three different species coexist in each location surveyed; across all species, 17 novel haplotypes were uncovered. Importantly, we also found that the populations at the six sites investigated were highly differentiated, suggesting that nearby islands may also harbour distinct populations and more unknown haplotypes. Our findings also identified several cox2–3 spacer farmed haplotypes of K. alvarezii (haplotype 3, SWAG) and K. striatus(haplotype 89), suggesting that escapees from farms reproduce in the wild and may potentially compete with the indigenous eucheumatoid population in East Malaysia. These results highlight a need to extend genetic surveys to other islands for discovering novel diversity and to extend the coverage of conservation policies. They also stress the importance of Malaysia acting now to develop its own cultivars by tapping into the country’s rich natural diversity, as well as assessing the risks of bioinvasion to the natural population via long-term biodiversity assessments.