Tributyltin (TBT) and triphenyltin (TPT) in different marine environmental compartments such as seawater, sediments, and inshore fishes were investigated in 21 Taiwanese harbors between 2001 and 2004 in order to determine the major factors influencing their distribution. The existence of major input sources and the limited water exchange rate inside the harbors were indicated by higher TBT concentrations in seawater from inner harbor than from outer harbor areas. The levels of TBT in sediments were found to be mainly affected by their geographic distribution, water exchange rates and shipping activity. No significant correlations in TBT concentrations between water, sediment and fish suggested TBT accumulation by fish might not result from water and sediment, but from their food. TPT were detected in most fish samples, but found in few sediment samples and none in seawater, indicating fish could be as a target element for monitoring contaminated levels of TPT in the aquatic environment. Mean concentrations of TBT in fish muscle higher than tolerable average residue levels (TARLs), and mean hazard indices of TBT and TPT higher than 1 suggested consumption of fishes from Taiwanese harbor areas might have potential high risk to human health.