Petromyzon marinus and Lampetra sp. are protected by international conventions (Bern, 1979; Habitats directive, 1992). To estimate the abundance, and thus the precariousness of each population, it is advisable to distinguish the larvae of each species, because they may use the same environments in rivers. However, these larvae were indistinguishable on morphological criteria (oral disk, pigmentation, myomeres,…). We used a molecular method for discriminating between P. marinus and Lampetra sp. A 560 bp DNA fragment of the mitochondrial cytochrome b (cyt b) gene was amplified by PCR. Restriction fragment length polymorphism (RFLP) analysis was performed using selected restriction enzymes. This test is useful for discriminating young lamprey larvae less 60 mm total length, which are frequently mixed in ammocoete habitats. Moreover, this developed test can be realized with 3 mm2 tissues (small piece of fin) only and does not require larvae sacrifice.