Until the middle of the twentieth century, malaria was frequently endemic in parts of Germany; Anopheles maculipennis complex species were considered the primary vectors. Three species of this complex have been identified in Germany: A. maculipennis s.s., Anopheles messeae and Anopheles atroparvus; the last predominantly from the coastal regions of Northern Germany. Anopheles daciae is a recently described member of the A . maculipennis complex and resembles the well-characterised species A. messeae, although the two species can be distinguished through their egg morphology and sequencing of the internal transcribed spacer 2 (ITS2) region of their nuclear rDNA. In this study, we harvested larval and adult mosquito samples from five breeding sites and ten CO(2) trap collection sites in the Upper Rhine Valley of Southwestern Germany to analyse the complement of anopheline species present. Mosquito ITS2 DNA was extracted and polymerase chain reaction (PCR)-amplified using established protocols. Genomic analysis was performed by a species-diagnostic restriction fragment length polymorphism assay as well as by sequencing of PCR products; the data obtained were aligned against nucleic acid sequences from English mosquitoes retrieved from GenBank. Additionally, the larval breeding sites of A. messeae were characterised through water quality measurement. Forty-seven samples were successfully processed, of which 6 were identified as A. daciae and 41 as A. messeae. All samples of A. daciae, which has not previously been found in Central Europe, originated from one CO(2) trap collection site in Dettenheim, close to Karlsruhe, Southwestern Germany. The identification of this malarial vector in a novel area may have implications for the re-emergence of disease subsequent to climatic changes.