Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.