| Summary: | In the previously published mitochondrial genome sequence of <i>Artemia urmiana</i> (NC_021382 [JQ975176]), the taxonomic status of the examined <i>Artemia</i> had not been determined, due to parthenogenetic populations coexisting with <i>A. urmiana</i> in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of <i>Artemia</i> (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to <i>A. urmiana</i> or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of <i>A. urmiana</i> with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of <i>A. urmiana</i>. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in <i>Artemia</i>, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among <i>Artemia</i> species. It is suggested that these markers should be included in future phylogenetic studies.
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