Three methods, tested on forest soil under two tree species (Abies alba and Pinus nigra), were compared in terms of quantity and quality of extracted DNA. The main reasons for the comparison were to ascertain the possibility of increasing DNA yields and to discriminate the genetic information located in different soil compartments (extra- and intracellular DNA). All DNA types were amplified with bacterial/fungal universal primers and PCR amplicons were separated by Denaturing Gradient Gel Electrophoresis (DGGE). The extracellular DNA, extracted by Alkaline Soil Washing, was about 70% of the total DNA, extracted by Mechanical Cell Lysis, while the combined sequential extraction, i.e. Alkaline Soil Washing followed by Mechanical Cell Lysis, extracted higher amounts of intracellular DNA. Each DNA fraction generated characteristic DGGE patterns. The separate fingerprinting of extra- and intracellular DNA was more complex than the fingerprinting of total DNA alone. The tree species affected the fingerprints but not the amounts of DNA extracted from soil. The sequential extraction allows to shed light on different DNA types, thus widening the knowledge of composition, history and distribution of soil microbial communities.