The SSU nuclear rDNA (encoding 18S ribosomal RNA) is one of the most frequently sequenced genes in the molecular analysis of insects. Molecular apomorphies in the secondary and tertiary structures of several 18S rRNA length-variable regions (LVRs) located within the V2, V4, and V7 hypervariable regions can be good indicators for recovering monophyletic groups within some heteropteran families. Among the LVRs that have been analysed, the LVR L in the V4 hypervariable region is the longest and most crucial for such assessments. We analysed the 18S rRNA V4 hypervariable region sequences of 45 species from the family Cydnidae, including all 6 subfamilies (Amaurocorinae, Amnestinae, Cephalocteinae, Cydninae, Garsauriinae, and Sehirinae) and three pentatomoid families (Parastrachiidae, Thaumastellidae, and Thyreocoridae), which have often been included in the broadly defined Cydnidae family. This is the first time that representatives of all Cydnidae subfamilies have been included in a molecular analysis. Only taxa from two subfamilies, Sehirinae and Cydninae, have been used in previous molecular studies. The secondary and tertiary structures of the LVR L were predicted for each species using the two-step procedure already accepted for such analyses to recover any molecular apomorphy essential for determining monophyly. The results of our comparative studies contradict the current understanding of the relationships among burrowing bugs and the current family classification.