The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons’ identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.