The population structure of Aulacomya atra and Mytilus chilensis was analysed at Station 1 (X-Huinay) in February 2012. Sampling of specimens was performed by Scientific SCUBA divers. Therefore, a quadratic frame (A. atra: 0.15 m2; M. chilensis: 0.09 m2) was placed in regular distances along horizontal transects. Four transects were sampled in the subtidal (5, 10, 15, 20 m) and one in the intertidal zone (at Mean Sea Level). All bivalves were collected from inside the frame and lengths were measured to the lowest 1 mm using a vernier caliper. Individuals only partly located inside the square were sampled on the upper and left margin, whereas excluded on the others.This dataset was generated in the frame of the co-operation between the Huinay Scientific Field Station (http://www.huinay.cl) and the Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research (http://www.awi.de).