The stratigraphy of bottom sediments was investigated in eastern waters of RupatStrait, Riau Province in June 2013. The analysis of sediment were conducted by twomethods i.e : grain-size analysis and ignition loss methods. The result showed that thevertical characteristic of bottom sediments changed irregularly. The vertical character-istic change of sediments was represented by the grain-size distribution, both verticallyand horizontally in the area. The similiarity of sediment characteristic among the sta-tions also represented by a cluster analysis. The cluster analysis showed that the sedi-ments were divided into four clusters which showed clearly the different of sedimentcharacteristic between station in this area.