Surface sediment samples were collected from Tanzanian major commercial ports and studied for the distribution and behavior of tributyltin (TBT) compounds and heavy metals. The content of TBT in sediments ranged from ND3670 ng (Sn) g1 dry wt (1780 ± 1720) (Mean ± SD) at Zanzibar and from ND16700 ng (Sn) g1 dry wt (4080 ± 7540) at Dar es Salaam ports, respectively. Maximum TBT levels were detected inside the both ports. Metabolic degradation of butyltin compounds (BTCs) showed that MBT + DBT > TBT %, this may be attributed by the warm ambient water and intense sunlight in the tropical regions. A sequential extraction procedure was undertaken to provide detailed chemical characteristics of heavy metals in the sediments. The procedure revealed that about 50 % of Fe in the both ports is in immobile fraction (residual fraction) while other metals; Cd, Cu, Ni, Co, Zn, Pb, and Mn were mostly found in exchangeable or carbonate fractions and thus can be easily remobilized and enter the aquatic food chain. This paper provides basic information of TBT compounds contamination and chemical characteristics of heavy metals in the marine ecosystem in Tanzania. To our knowledge, this is the first documentation of Organotin compounds (OTCS) in marine environments in East Africa and suggests the importance of further detailed OTCS studies in other sub Saharan Africa regions.