Bivalve veligers are difficult to identify morphologically, and when it comes to strait hinge (~90 μm) or small velichoncha veligers (>90–300 μm) it is practically impossible. However, the use of new molecular based methods allows the identification of individual larvae, in a size independent manner (Larsen et al. 2005). In this contribution we show small-scale spatial variations among species of velichoncha veligers, in the size range of 120–135-μm shell length. Larvae were sampled quasi-simultaneously in a squared matrix at Løgstør Broad, Limfjorden, Denmark. The matrix consisted of 46 sampling sites, situated within 500–750 m apart. Velichoncha larvae were enumerated and sized. Larval concentrations ranged from <50 to >350 Ind. per liter, and found not to be coupled to any environmental parameter recorded. At 25 of the sampling sites larvae were identified to species/genera level by Singe Step Nested Multiplex PCR (SSNM-PCR). The bulk of the velichoncha was Mytilus edulis/Musculus marmoratus (52% to 91%), which was found to be present in all samples tested. In contrast Ensis spp. was observed in 24 of the tested samples, making up between 4% to 31%, whereas species of the order Myoida and species belonging to the Cardiidae family only was observed occasionally in low relative abundance. At a few sampling sites a difference in the vertical distribution among the composition of velichoncha assemblages was suggested. Hence, SSNM-PCR was useful for identifying evidence for spatial scale differences in species composition within bivalve larval assemblages. Because of the ecologic and economic importance of some species, there are significant perspectives in identifying bivalve veligers in large scale studies.