A Joint Research Agreement (JRA) on the Characterization and Evaluation of Plant Genetic Resources for Food and Agriculture was made in June 2015 between the National Institute of Agrobiological Sciences (NIAS) of Japan and the Nepal Agricultural Research Council of Nepal. All obligations and rights of the NIAS under the JRA were transferred to the National Agriculture and Food Research Organization (NARO), owing to the merger of the NARO and NIAS in April 2016. Based on the agreement, the first collaborative survey for Amaranthus and Capsicum genetic resources in Nepal was carried out from 12th to 23rd February 2016 in the districts of Rasuwa, Kathmandu, Lalitpur, Bhaktapur, and Kavre in the Central Development Region. During the survey, a total of 88 samples were collected, including 15 Amaranthus samples and 42 samples of Capsicum samples. These materials were conserved in the gene bank of Nepal. Using the Standard Material Transfer Agreement (SMTA), a subset of the 87 samples, with the exception of an Oryza sativa L. sample, was transferred to NARO gene bank in Japan.