Over the past few years the High Throughput Sequencing technologies have become well established in modern biology and medicine. Fundamentally new opportunities for genome sequencing and in-depth analysis of various DNA and RNA libraries have been discovered. However, new technologies come with new pitfalls such as limitations in obtaining valid qualitative and quantitative data in the in-depth analysis of complex libraries. A clear understanding of these limitations is necessary for the accurate interpretation of the collected data as well as for the search for technological solutions to minimize their impact. The following review shows how molecular barcoding helps normalize samples efficiently and eliminate PCR and sequencing errors while preserving the actual diversity of libraries in the course of HTS analysis of complex libraries.