Cdk5 is a serine/threonine kinase that plays a pivotal role in neural development. Activation of Cdk5 requires its association with its activator, p35 or p39. More than forty proteins have been identified as the substrates for Cdk5. By phosphorylating these diverse cellular targets, Cdk5 plays a multifunctional role in nervous system including neurite outgrowth, axonal guidance, cytoskeleton assembly, membrane transport, synaptic function and dopamine signaling. In addition, recent studies have implicated that Cdk5 is involved in the regulation of gene transcription. For example, our laboratory has reported that a transcription factor, signal transducer and activator of transcription-3, and a transcription regulator, mSds3, are the substrates for Cdk5. Using yeast two-hybrid screen, we identified ANKRA2 (ankyrin repeat-containing protein, family A, member 2), a protein potentially involved in the regulation of transcription, as a p35-interacting protein. We confirmed the association of ANKRA2 with p35 using glutathione S-transferase pull-down assay as well as co-immunoprecipitation analysis. Importantly, we found that ANKRA2 is the substrate for Cdk5. We showed that ANKRA2 interacts with distinct members of histone deacetylase (HDAC) and is associated with HDAC activity. Expression of ANKRA2 represses the transcriptional activity of microtubule associated protein 1A (MAP1A) in neuroblastoma cells whereas p35 augments the repression ability of ANKRA2. Taken together, these findings identify ANRKA2 as a novel substrate of Cdk5 and provide insights into understanding how Cdk5 regulates gene transcription in the nervous system.