The complete mitogenomes of Cyrtarachne nagasakiensis and Hypsosinga pygmaea are determined to be 14,402 and 14,193 bp in length, with the A + T content of 75.7% and 76.1%, respectively. All protein-coding genes in both spiders start with the initiation codons (ATT, ATA, TTA or TTG) that are usually used in Araneae mitogenomes, and terminate with canonical stop codon TAA or TAG except for ND5 in both spiders and ND4L in H. pygmaea, which end with the incomplete codon TA or T instead. Most of the tRNAs lack the potential to form the typically cloverleaf-shaped secondary structures and none of tandem repeats are present in the control regions of both spider mitogenomes. The phylogenetic analysis based on the Bayesian inference dataset shows a good resolution of relationship of C. nagasakiensis and H. pygmaea in Araneidae.