Mitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dynamics, and investigating how environmental pressures shape traits underpinned by genetic variation. Here, we present the bioinformatic pipeline and code used to assemble and annotate the complete mitogenomes of five houndsharks (Chondrichthyes: Triakidae) and compare them to the mitogenomes of other closely related species. We demonstrate the value of a combined assembly approach for detecting deviations in mitogenome structure and describe how to select an assembly approach that best suits the sequencing data. The datasets required to run our analyses are available on the GitHub and Dryad repositories. Key features • Tips and code for conducting de novo, reference-based, and hybrid assembly. • Guide to detecting deviations in the structure of the mitochondrial genome. • Step-by-step guide to annotating and comparing the characteristics of mitochondrial genomes. • Access to the scripts, data files, and pipelines used to enable replication of all analyses.