Puncta adherentia junctions (PAJs) have been observed at glutamatergic excitatory synapses on glutamatergic excitatory neurons (E→E synapses) in the mouse hippocampus and are considered to be the mechanical adhesion sites between axon terminals and dendritic shafts. However, it remains unclear whether they are present at other types of synapses, such as glutamatergic synapses on GABAergic inhibitory neurons (E→I synapses) and GABAergic synapses on excitatory neurons (I→E synapses) and inhibitory neurons (I→I synapses). We showed here that the PAJ components, such as nectin-1, nectin-3, l-afadin, N-cadherin, β-catenin, and αN-catenin, were observed at all four types of synapses in cultured mouse hippocampal neurons. In the adult mouse hippocampus, these PAJ components were observed at a subset of I→I synapses on parvalbumin-positive GABAergic inhibitory neurons, similarly to their presence at E→E synapses in the CA1 and CA3 regions. In contrast, several PAJ components, including nectin-3, l-afadin, N-cadherin, β-catenin, and αN-catenin, were observed at E→I and I→E synapses, whereas nectin-1 was absent. These results indicate that the PAJs are formed at a subset of I→I synapses in addition to E→E synapses, where all examined PAJ components are present, whereas E→I and I→E synapses exhibit only partial localization of these components, reflecting molecular diversity among different synapses in the adult mouse hippocampus.