The chlorocruorin of the polychaete Eudistylia vancouverii observed in the electron microscope in vitreous ice, was subjected to a three-dimensional (3D) reconstruction by the random conical tilt series method. The 3D volume with a resolution of 35 A reconstructed from 1062 images in top, side and intermediate view orientations has a D6 point-group symmetry. It possesses the characteristic hexagonal bilayer (HBL) appearance. Each hexagonal half-molecule comprises size hollow globular substructures (HGS) presumed to correspond to the dodecameric subunits. In projection, when the molecule is viewed along its 6-fold axis, the two halves are not perfectly eclipsed. The vertices of the upper hexagonal layer are 14 degrees rotated clockwise compared with those of the lower half. At a threshold displaying 100% of the expected molecular volume, the 3D volume contains in its center a flat hexagonal central mass disconnected from the rest of the volume. Several types of connections, termed c1 through c4, are visible between the HGSs. The c1 and c2 connections link the HGSs of the same hexagonal half-molecule. The c3 connections make a hexagonal inner bracelet linking the HGSs of each half-molecule. The c4 connections link pairs of HGSs superposed in the two hexagonal layers. Because of the half-molecules rotation around the 6-fold axis, the two HGSs linked by a c4 connection are not exactly superposed. It is proposed that the c3 and c4-connection bodies and less probably the flat central hexagonal mass are composed of chloroheme-deficient linker chains. When eroding the 3D volume by raising the threshold, the HGS appears composed of three elongated structures likely containing four globin chains. In addition, they show an approximate 3-fold symmetry. At high thresholds, two of these masses, dumbbell-shaped, separate into globular masses while the third structure remains compact as long as 1% of the molecular volume is displayed.