The present study aimed to evaluate how the presence of hydrocarbons effects the abundance of heterotrophic bacteria, cyanobacteria and yeasts in estuarine sediments and waters of two distinct regions, Santos and Rio Itanhaém estuaries, both in terms of environmental characteristics and in relation to the degree of contamination and to isolate microorganisms, with an emphasis on yeasts, as potential bioindicators of contamination by petroleum hydrocarbons and as bioremediators of estuarine sediments.