MitoFinder is a user-friendly bioinformatics pipeline developed to efficiently assemble and annotate mitogenomic data from hundreds of ultraconserved element (UCE) libraries. The study demonstrates that metagenomic assemblers, particularly MetaSPAdes, are well-suited for assembling both UCEs and mitochondrial DNA (mtDNA) from target enrichment sequencing data. Using ants (Formicidae) as a case study, where 501 UCE libraries were sequenced but only 29 mitogenomes were available, MitoFinder successfully extracted mtDNA signal from all UCE libraries, allowing for species identification via CO1 barcoding. The pipeline retrieved 296 cases where the mitochondrial genome was assembled in a single contig, significantly increasing the number of available ant mitogenomes. MitoFinder also enabled the detection of potential mitonuclear discordance, which can result from hybridization or introgression events. The software is available on GitHub and provides a powerful tool for extracting complementary mitogenomic data from UCE libraries, applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing. The study highlights the importance of mitochondrial data in phylogenetic analysis, species identification, and detecting hybridization events, while also addressing challenges such as cross-contamination and NUMT (nuclear mitochondrial DNA) artifacts. The results show that mitochondrial data can be effectively recovered from UCE sequencing data, offering valuable insights into evolutionary relationships and phylogenetic discordance. MitoFinder represents a significant advancement in the efficient and accurate assembly of mitochondrial genomes from UCE libraries, providing a robust solution for phylogenomic studies in diverse taxa.MitoFinder is a user-friendly bioinformatics pipeline developed to efficiently assemble and annotate mitogenomic data from hundreds of ultraconserved element (UCE) libraries. The study demonstrates that metagenomic assemblers, particularly MetaSPAdes, are well-suited for assembling both UCEs and mitochondrial DNA (mtDNA) from target enrichment sequencing data. Using ants (Formicidae) as a case study, where 501 UCE libraries were sequenced but only 29 mitogenomes were available, MitoFinder successfully extracted mtDNA signal from all UCE libraries, allowing for species identification via CO1 barcoding. The pipeline retrieved 296 cases where the mitochondrial genome was assembled in a single contig, significantly increasing the number of available ant mitogenomes. MitoFinder also enabled the detection of potential mitonuclear discordance, which can result from hybridization or introgression events. The software is available on GitHub and provides a powerful tool for extracting complementary mitogenomic data from UCE libraries, applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing. The study highlights the importance of mitochondrial data in phylogenetic analysis, species identification, and detecting hybridization events, while also addressing challenges such as cross-contamination and NUMT (nuclear mitochondrial DNA) artifacts. The results show that mitochondrial data can be effectively recovered from UCE sequencing data, offering valuable insights into evolutionary relationships and phylogenetic discordance. MitoFinder represents a significant advancement in the efficient and accurate assembly of mitochondrial genomes from UCE libraries, providing a robust solution for phylogenomic studies in diverse taxa.