MitoFinder is a user-friendly bioinformatic pipeline designed to efficiently assemble and annotate mitogenomic data from hundreds of ultraconserved element (UCE) libraries. The pipeline was developed to address the lack of mitogenomic data in capture-based studies, which often sequence mitochondrial DNA (mtDNA) alongside targeted loci. Using ants (Formicidae) as a case study, the authors compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. They found that metagenomic assemblers, particularly MetaSPAdes, are well-suited for assembling both UCEs and mtDNA. MitoFinder successfully extracted mtDNA signal from all 501 UCE libraries, allowing species identification using CO1 barcoding. Additionally, the automated procedure retrieved 296 cases where the mitochondrial genome was assembled in a single contig, increasing the number of available ant mitogenomes by an order of magnitude. The approach is potentially applicable to other sequence capture methods, transcriptomic data, and whole-genome shotgun sequencing in diverse taxa. The MitoFinder software is available on GitHub and GitLab.MitoFinder is a user-friendly bioinformatic pipeline designed to efficiently assemble and annotate mitogenomic data from hundreds of ultraconserved element (UCE) libraries. The pipeline was developed to address the lack of mitogenomic data in capture-based studies, which often sequence mitochondrial DNA (mtDNA) alongside targeted loci. Using ants (Formicidae) as a case study, the authors compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. They found that metagenomic assemblers, particularly MetaSPAdes, are well-suited for assembling both UCEs and mtDNA. MitoFinder successfully extracted mtDNA signal from all 501 UCE libraries, allowing species identification using CO1 barcoding. Additionally, the automated procedure retrieved 296 cases where the mitochondrial genome was assembled in a single contig, increasing the number of available ant mitogenomes by an order of magnitude. The approach is potentially applicable to other sequence capture methods, transcriptomic data, and whole-genome shotgun sequencing in diverse taxa. The MitoFinder software is available on GitHub and GitLab.