Mutations give rise to the variation that is seen across all levels of biological organisation. Microevolution, i.e. the collective process that changes allele frequencies in populations, acts on the lower levels of the hierarchy of levels of biological organisation and operates over short timescales. Thus microevolutionary studies represent the basis for evolution at the population and species level. This thesis investigates how microevolution acts on different levels of biological organisation, i.e. molecule (Section 6), organelle (Section 5), cell (Section 5), tissue (Section 5), organism (Section 5), population (Section 3 & 4) and species (Section 2). Mitochondrial DNA is commonly used in population and conservation genetics studies because of its high mutation rate that typically translates into high resolution analyses of evolutionary mechanisms and processes over short time scales. Two different methods are presented that facilitate the recovery of complete mitochondrial genomes. The first uses only three primer pairs and is designed to amplify the mitochondrial genome for any avian species. The method can be adapted to amplify the mitochondrial genomes for any animal class using the super conserved prime site principle. The second method uses the endonuclease RecBCD to digest the linearised nuclear DNA in a whole blood DNA extract, leaving only the circular mitochondrial genomes. This method is potentially applicable to the study of any animal species and has the advantage of recovering the true mitochondrial genotype frequencies, due to the absence of amplification bias. Both methods can thus greatly facilitate the recovery and characterisation of mitochondrial genomes in combination with second generation sequencing. The recovery of complete mitochondrial genomes allows the study of microevolution at high resolution and thus increases confidence in subsequent analyses.