The content of Mn, Zn, Ni, Cu, Fe, and Pb in 10 samples of Kappaphycus alvarezii (cottonii) and 10 samples of Eucheuma denticulatum (spinosum) from 15 different sites in the intertidal coastal area of Zanzibar were determined by using EDXRF. The heavy metals assessed in both species decreased in the order of Fe >Mn > Zn >Pb> Cu > Ni. In general, the cottonii samples in Unguja had significantly higher (p ≤ 0.05) concentrations of Fe, Zn, Ni, Cu and Pb than the spinosum samples, but the latter had significantly higher levels of Mn. Similarly, the cottonii samples in Pemba had significantly higher (p ≤ 0.05) concentrations of Ni, Cu and Pb than the spinosum samples, but the latter had significantly higher levels of Fe and Zn. The concentrations of heavy metals in cottonii and spinosum in the present study were noticed lower compared to publish results. The results from this study revealed that, the heavy metals contaminations in cottonii and spinosum along the coastal area in Zanzibar were mainly caused by effluents that directly flow into marine environments. Hence, serious measures should be taken to reduce the flow of waste effluents into the marine ecosystem.