Recently, considerable commercialization of services for quantification of gut microbiota aimed to diagnose dysbiosis, the microbial imbalance, is observed. In the context of growing interest to the personalized approaches in medicine and preventive therapy, the diagnosis of dysbiosis is becoming increasingly important. The results of such screening are used to adjust guidelines on correction of the diet, lifestyle modification, or, where necessary, drug therapy prescription. Such assessment requires a reliable and accurate method for evaluation of microbiota, since validity of further recommendations and therapeutic interventions depends on the quality of the data obtained. The paper reports the main aspects of the two approaches used for microbiota quantification: 16S rRNA next-generation sequencing (16S NGS) and real-time PCR (qPCR). The strengths (from our perspective) and weaknesses of the approaches are also provided.