Synaptic junction (SJ) fractions were isolated from the brains of the gray shark, bonito, common frog, several reptiles, and common chicken and compared to those prepared from mammalian brain. All SJ preparations, as judged by electron microscopic analysis, were at least 85% pure, consisting primarily of postsynaptic densities (PSDs) with or without an overlying plasma membrane and, to a lesser extent, of complete synaptic junctions. Complete junctions were less abundant in preparations from lower vertebrates. The electrophoretic pattern of SJs from different vertebrate species showed considerable conservation of the major protein bands. The most abundant were fibrous proteins, especially tubulins, actin, and the PSD-specific polypeptide with a molecular weight of 52,000 (PSD-52). Glycoproteins capable of binding concanavalin A were present in SJs from all vertebrates; their apparent molecular weight and relative abundance were characteristic of each animal order examined, showing more similarities in species more closely related phylogenetically. Finally, a protein (antigen PSD-95) previously shown to be located specifically in the postsynaptic densities of the mammalian brain was present in all species. The binding of antibody specific to this protein decreased with descending phylogenetic order from mammals to shark. Nonetheless, PSD-95 was present in all vertebrate species and appeared to be a general specific marker for PSDs.