Characteristics and Evolutionary Relationships of Two Mitochondrial Genomes of Iguanodectes (Characiformes, Iguanodectidae)

<i>Iguanodectes geisleri</i> and <i>I. adujai</i> are freshwater fish from South America. Their taxonomic status and phylogenetic relationships are uncertain due to limited molecular data. High-throughput sequencing was applied to obtain and annotate for the first time the complete mitochondrial genomes of <i>I. geisleri</i> and <i>I. adujai</i> to clarify their phylogenetic positions. Mitochondrial genome sequences of 73 Characoidei species were retrieved from GenBank, with <i>Gyrinocheilus aymonieri</i> and <i>Microphysogobio alticorpus</i> designated as outgroups. Phylogenetic trees were constructed using a mitochondrial protein-coding gene dataset and Maximum Likelihood and Bayesian Inference methods. The complete mitochondrial genome measured 16,774 and 16,802 bp, respectively. Both genomes exhibited highly conserved structures. Despite morphological similarities and a close phylogenetic relationship, differences were detected in genomic structure, base composition, codon usage bias, and the control region between the two species. The two species comprise a strongly supported monophyletic clade and are sister species but represent distinct, independent branches. <i>I. geisleri</i> and <i>I. adujai</i> have been recognized as distinct species based on morphological differences, and this study provides molecular confirmation of their separate taxonomic status. The study provides molecular data for the taxonomic identification of fishes of the genus, <i>Iguanodectes</i>, and foundational mitochondrial genomic data for Characiformes. The study advances research on the genetic evolution of this group and resource conservation.