Telomeric sequences in the insect infraorder Nepomorpha (Hemiptera: Heteroptera) have previously been characterized only in the basal superfamily Nepoidea, where the canonical arthropod motif (TTAGG)n was confirmed by fluorescence in situ hybridization (FISH). The telomeric repeat composition of the remaining Nepomorpha superfamilies remained unknown. Using TREW, a tool for de novo identification of candidate telomeric sequences from short-read whole-genome sequencing data, we screened 32 publicly available NCBI datasets representing 24 genera and all 13 Nepomorpha families. The method was validated against species with known (TTAGG)n telomeres in Nepoidea, successfully recovering the expected motif. In Corixoidea, (TTAGG)n was uniformly identified as the best candidate for telomeric sequence across all eight species of three families – Corixidae, Diaprepocoridae and Micronectidae. In contrast, derived 10-bp motifs were recovered from the remaining four superfamilies: (TGGTTAGTGA)n and (TGGTTAGTGT)n in Ochteroidea, (TGGATAGGTG)n and (TGGATAGGAG)n in Naucoroidea (including Aphelocheiridae and Potamocoridae), and (TGGATAGGGT)n uniformly across Notonectoidea and Pleoidea. All derived decamers except those from Ochteroidea share the core octamer TGGATAGG. The retention of (TTAGG)n in the two basal superfamilies and the occurrence of derived decamers in more derived clades are congruent with most current phylogenetic hypotheses for Nepomorpha and support independent evolution of 10-bp motifs within the infraorder. The presence of an identical candidate for telomeric sequence – (TGGATAGGGT)n in Notonectoidea and Pleoidea provides additional support for their close phylogenetic relationship and might be a synapomorphy for this clade. These findings extend the known pattern of telomeric diversification within Heteroptera to Nepomorpha and demonstrate the utility of short-read archival data for taxonomic surveys of telomeric composition.