Molecular methods are becoming increasingly important in systematic acarology. In this review I describe the properties of the ideal molecular marker and compare these with genes that have been used for phylogenetic studies of mites and ticks. The second internal transcribed spacer of the nuclear ribosomal gene cluster (ITS2) and the mitochondrial protein-coding gene cytochrome oxidase I (COI) together provide a powerful tool for phylogenetics at low taxonomic levels. The nuclear ribosomal genes 18S and 28S rDNA are equally powerful tool for phylogenetics at the deepest levels within the Acari. What appear to be lacking are markers that are useful at intermediate levels. The mitochondrial ribosomal genes 12S and 16S rDNA have not lived up to their initial promise. I suggest some nuclear protein-coding genes that may be suitable alternatives. Methods for collection and storage of mites for molecular work, DNA extraction and phylogenetic analysis are also briefly discussed.