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Traditional Chinese medicines (TCMs), a key branch of natural medicines, play an important role in the treatment of diseases because of their reliable clinical performance. Identification of their active compounds constitutes a bottleneck in the development of TCMs. Screening and analysis of active compounds is a challenge in TCM research. This review summarizes recent progress in the development of biological fingerprinting strategies for screening and analyzing bioactive compounds in TCMs using molecular recognition, metabolism and omics tools. The evaluated strategies include the following techniques: microdialysis/centrifugal ultrafiltration-HPLC, biochromatography, metabolic fingerprinting analysis, 2-dimensional biochromatography and omics fingerprinting analysis.