This study examined whether Lactobacillus rhamnosus GG (LGG) and Bifidobacterium bifidum TMC3115 (TMC3115) could morphologically or physiologically influence hippocampal neuronal development in vitro. Hippocampal neurons cultured in vitro were exposed to live or heat-inactivated LGG or TMC3115 for either 6 or 24 h. Neuronal morphological changes and drebrin (DRB) and synaptophysin (SYP) protein levels were monitored using immunofluorescence. And the levels of DRB, SYP, and brain-derived neurotrophic factor (BDNF), and cAMP-response element binding protein (CREB) mRNA were detected using RT-PCR. The BDNF, CREB, and phosphorylated-CREB (P-CREB) protein levels were detected by extraction-enzyme-linked immunosorbent assay (ELISA) or Western blot assays. Heat-inactivated LGG and TMC3115 could enhance neuron viability, DRB and SYP protein levels, and BDNF mRNA level were significantly altered after exposure to the tested bacteria with 6 h or 24 h. There were no significant differences in neuronal morphology or DRB, SYP, or CREB mRNA levels among the groups following bacterial exposure. However, following exposure of live TMC3115 for 24 h, the neuronal BDNF and P-CREB protein levels were both significantly up-regulated as detected by western blot assays. These results demonstrated that LGG and TMC3115 could affect neuronal viability, along with hippocampal synaptic and functional development, in a strain-dependent manner, which may also be closely associated with the physiological and culture conditions of each strain. Up-regulated P-CREB may be one of the underlying mechanisms by which the bacteria, especially neurons following exposure of live TMC3115 for 24 h, are able to regulate neuronal BDNF protein production.