Microbiome research is becoming increasingly relevant in both medicine and other socially significant areas, including agriculture, food security, and ecology. Many studies associate dysbiotic changes in the gut microbiome and other human organs with the development of pathological conditions. For instance, changes in the gut microbiota have been associated with the development of cardiovascular and respiratory diseases, which are the leading causes of death worldwide. The development of rapid screening methods for complex microbiome dynamics may in the future become the methods of choice for early diagnosis and monitoring the progression and effectiveness of treatment for microbiome-associated diseases in clinical diagnostic centers. This review article will examine the main currently proposed approaches to microbiome fingerprinting, including denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, terminal restriction fragment length polymorphism, automated rRNA intergenic spacer analysis, single-strand conformation polymorphism, amplicon length heterogeneity-PCR, cytometric fingerprinting, and high-resolution melting curve analysis. We compare the advantages and disadvantages of these methods, assess their potential for rapid screening of microbiome composition changes, and propose directions for further research in this area.