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The complete mitochondrial genome of Zyginella minuta was sequenced and annotated in this study. The closed-loop mitogenome is 15,544 bp in length, has an A + T content of 76.3% (A = 43.0%, T = 33.3%, G = 10.2%, and C = 13.5%), containing 37 typical genes and a control region. All protein-coding genes (PCGs) started with ATN and stopped with TAA, except for ATP8 used TTG as initiation codon, Cytb ended with TAG, ND5, and ND4 used incomplete T as stop codon. The resultant phylogeny using 13 PCGs and 2 rRNAs showed these species in Typhlocybinae including Z. minuta formed a cluster indicating closer relationship than others.