Neurons are characterized by subcellular compartments such as axons, dendrites and synapses that have highly specialized morphologies and biochemical specificities. Cortactin binding protein 2 (CTTNBP2), a neuron-specific F-actin regulator, has been shown to play a role in the regulation of dendritic spine formation and maintenance. Here, we show that in addition to F-actin, CTTNBP2 also associates with microtubules before mature dendritic spines formed. The association of CTTNBP2 and microtubules induced the formation of microtubule bundles. Although the middle (Mid) region of CTTNBP2 was sufficient for association with microtubules, for microtubule bundling, the N-terminal region containing the coiled coil motifs (NCC) mediating the dimerization or oligomerization of CTTNBP2 is also required. Our study indicates that CTTNBP2 proteins form a dimer or oligomer and bring multiple microtubule filaments together to form bundles. In cultured hippocampal neurons, knockdown of CTTNBP2 or expression of the Mid or NCC domain alone reduced the acetylation levels of microtubules and impaired dendritic arborization. The study suggests that CTTNBP2 influences both the F-actin and microtubule cytoskeletons and regulates dendritic spine formation and dendritic arborization.