Soil contamination with petroleum derivatives, including polycyclic aromatic hydrocarbons (PAHs), is an increasing problem in various parts of the world. Dynamics of bacterial communities were examined in different petroleum-contaminated soils to assess patterns of microbial responses to PAH contamination. Bacterial community fingerprints were determined using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene as a molecular marker. Sequence-based identification of dominant DGGE bands in petroleum hydrocarbon-contaminated soils revealed the presence of Pseudomonas sp., P. pseudoalcaligenes, P. nitroreducens, P. toyotomiensis, and uncultured Pseudomonas clones as the dominant bacterial groups. In a laboratory scale microcosm, prolonged incubation of contaminated soils resulted in marked deterioration of bacterial communities. DGGE fingerprints of PAH-amended microcosms indicated the presence of distinct bands corresponding to hydrocarbon-degrading bacteria, such as P. mendocina, Cellulosimicrobium sp., Stenotrophomonas sp., and Sphingobacterium sp., which were barely detected in unamended soils. Bacterial community structure in amended soils remained stable even after prolonged incubation up to 6 months. Catabolic genes for upper aromatic hydrocarbon metabolism, such as those encoding naphthalene dioxygenase, toluene dioxygenase (todC1), and Rieske-type proteins of dioxygenases and lower pathway genes encoding catechol 1,2-dioxygenase and catechol 2,3-dioxygenase (C23O and xylE) were used as biomarkers for monitoring PAH biodegradation in constructed microcosms. Among all tested primer sets, those for C23O and naphthalene dioxygenase allowed efficient amplification of extradiol ring cleavage dioxygenase and naphthalene dioxygenase, respectively, from soil samples amended with naphthalene as a model PAH compound.