During a French biomonitoring survey of the lakes in the region Rhône-Méditerranée-Corse, a large, unknown Gomphonema taxon was observed in a lake in the vicinity of the City of Lyon (Département du Rhône, France), that could not be identified using the currently available literature. Detailed light and scanning electron microscopy investigations revealed the presence of two types of valves, one bearing a thick marginal crest and valves lacking the crest. Following comparison with similar, mostly tropical Gomphonema species, the unknown taxon is described as new: Gomphonemavancampianumsp. nov. Discriminating features of the new species include the peculiar valve shape resembling a Chinese spoon, the broad upper valve part with acuminate tip, the presence of shallow depressions in the axial area, distinctly punctate striae and the occasional presence of the marginal crest. The new species was observed in several samples collected in an oligo- to mesotrophic, calcium-carbonate rich lake with a high ecological quality.