Leukocyte common antigen-related receptor tyrosine phosphatases (LAR-RPTPs) are evolutionarily conserved presynaptic organizers. The synaptic role of vertebrate LAR-RPTPs in vivo, however, remains unclear. This study systematically analyzed the effects of genetic deletions of LAR-RPTP genes by generating single conditional knockout (cKO) mice targeting PTPσ and PTPδ. Although the numbers of synapses were reduced in cultured neurons deficient in individual PTPs, abnormalities in synaptic transmission, synaptic ultrastructures, and vesicle localization were observed only in PTPσ-deficient neurons. Strikingly, loss of presynaptic PTPσ reduced neurotransmitter release prominently at excitatory synapses, concomitant with drastic reductions in excitatory innervations onto postsynaptic target areas in vivo. However, postsynaptic PTPσ deletion had no effect on excitatory synaptic strength. Furthermore, conditional deletion of PTPσ in ventral CA1 specifically altered anxiety-like behaviors. Taken together, these results demonstrate that PTPσ is a bona fide presynaptic adhesion molecule that controls neurotransmitter release and excitatory inputs.11 100 nm from the presynaptic AZ membrane, was significantly increased in PTPσ-deficient presynaptic terminals (Fig 2E). In contrast, the number of tethered vesicles, defined as vesicular structures docked at presynaptic AZ membranes, was only marginally increased, an increase that was not statistically significant (Fig 2F). Surprisingly, the AZ length was increased by ~30% (Fig 2A and 2B), similar to the doubled AZ size in Caenorhabditis elegans mutants lacking ptp-3A, an orthologue of the type IIa RPTP gene (Ackley et al, 2005, Han et al, 2019. Consistent with this, a corresponding increase (~15%) in PSD length was observed (Fig 2A and 2C). This phenotype was not observed in PTPδ-deficient presynaptic terminals, nor were there any alterations in other anatomical parameters (Fig 2H-2M). Quantitative immunoblot analysis of PTPσand PTPδ-deficient neurons showed comparable expression of presynaptic AZ and PSD proteins, although the level of RIM1/2 was significantly lower in PTPδ-deficient neurons (Fig 2G, 2N, Appendix Fig 3A and 3B). These results suggest that PTPσ and PTPδ are not functionally redundant, and that PTPσ, but not PTPδ, is crucial in controlling the structural organization of both presynaptic AZs and PSDs.