Culex pipiens s.s. is one of the most common mosquito found breeding in human habitats throughout the temperate northern hemisphere. The species is easily confused with Culex torrentium as they only differ by a few subtle morphological characteristics. Further, Culex pipiens biotypes, which are morphologically indistinguishable, are known vectors of West Nile virus (WNV) and several other arboviruses. We used DNA barcoding methods to assess the occurrence and diversity of Cx. torrentium and Cx. pipiens s.s., as well as Cx. pipiens biotypes molestus and pipiens and their hybrids, in Belgium. During a nationwide monitoring program (MEMO, Monitoring of Exotic Mosquitoes), 31 selected sites in Belgium were monitored over three consecutive years (2017-2019) for the introduction of exotic mosquitoes (Diptera: Culicidae). 34,401 collected mosquito samples (adults, larvae) were morphologically identified as Culex pipiens/Cx. torrentium, of which 1689 specimens were selected at random for species identification using DNA barcoding. In the present study, a total of 401 Culex torrentium and 1248 Culex pipiens s.s. were DNA barcoded (956 biotype pipiens, 227 biotype molestus, and 29 hybrids). Based on the alignments of the generated sequences (COI) analyses were run in Arlequin to assess the genetic diversity. The results confirm that both species are widespread in Belgium. Pipiens biotype hybrids were found in 13 sites where both biotypes occurred in sympatry. While Cx. torrentium sequences revealed many COI haplotypes, Cx. pipiens s.s. showed only one abundant haplotype. This latter observation may either reflect a recent population-wide demographic or range expansion, or a recent bottleneck, possibly linked to a Wolbachia infection. Additionally, new evidence is provided for the asymmetric but limited introgression of the molestus biotype into the pipiens biotype.