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To date classification and differentiation of Alaria spp. are based largely on external characteristics and comparative morphology of adult flukes. The accurate differentiation between various Alaria spp. mesocercariae is indeed difficult because there are only few data on morphological and morphometrical features of the parasite's developmental stages. We established a conventional polymerase chain reaction (PCR) for a molecular-based diagnosis of Alaria alata mesocercariae that can aid in their identification. Twenty Alaria spp. mesocercariae specimens were collected from three different wild boars originating from different areas of eastern Germany. DNA from the prepared isolates was extracted, and a primer pair was selected to amplify a 303-bp region of the A. alata genome. The DNA preparations extracted from the field samples as well as A. alata positive controls were successfully amplified and yielded a single sharp band of the expected size. In all samples, molecular identification was consistent with morphological identification. With our new PCR assay, we present the first approach for identification and characterization of A. alata mesocercariae specimens using molecular methods. This practicable and reproducible protocol can be used for both diagnostic and epidemiological purposes.