Although previous studies have indicated that various brain areas involve in the acquisition of associative learning, it still remains unclear how the neural circuitry system regulates the learning processes. In order to clarify these mechanisms, we have developed retrograde vectors which are applicable as an approach for the study of neural circuits based on brain functions by combining with cell targeting, opto/chemogenetics in selective neural pathways. By using these methods, we addressed the roles of the pathways originating from the parafascicular nucleus (PF) and central lateral nucleus (CL) in the intralaminar thalamic nuclei to the striatum in mice. Interestingly, these two pathways control both the acquisition and performance of visual associated discrimination. In addition, the elimination of the CL-derived thalamostriatal neurons impaired the behavioral switching flexibility through the reversal and the set shifting tasks. Our data suggest that the PF and CL thalamostriatal systems are involved in cognitive function of basal ganglia circuitry, and that these two circuits possess distinct roles in the control of behavioral selection and flexibility.