This practitioner’s manual is the complement to the recently published volume ‘Molecular Systematics and Evolution: Theory and Practice’ and focuses on recently developed techniques for data acquisition and analysis in molecular systematics and evolutionary biology. The first section examines analytical methods in chapters dealing with DNA sequence alignment optimisations, techniques for analysing large data sets as implemented in the program TNT, measures of support and data partitions. Approaches that will develop further in the next few years are also covered and the reader is subsequently exposed to chapters on genome databases and comparative phylogenomics. The second section is dedicated to obtaining and archiving specimens for molecular work and laboratory methods. Future developments are again included by chapters on high-throughput DNA sequencing and in situ hybridisation techniques. Due to the detailed protocols on DNA isolations of plants, algae, animals and bacteria from both fresh, silica-dried and ancient museum material, various PCR methods, microsatellite analysis and information on web-located sites, both systematists and evolutionary biologists can find a lot of information in this manual about modern molecular data collection techniques. In addition, molecular biologists might get ideas on how their data can be analysed in an evolutionary context.