Based on the agreement between the National Agriculture Genetic Resources Center (NAGRC), Nepal Agricultural Research Council (NARC), Nepal, and the Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Japan, we began the second collaborative exploration for Amaranthus and Capsicum genetic resources in Nepal following the first one, which was conducted in the Mid and Far Western Development Region from October 29 to November 10, 2016. In this survey, a total of 98 samples were collected. Among them, 28 samples were of Amaranthus spp.—24 of A. hypochondriacus, two of A. caudatus; and two of weedy amaranths (Amaranthus spp.)—and 36 Capsicum spp.—33 of C. annuum and three of C. frutescens. All samples were conserved in the gene bank of NAGRC, Nepal. A subset was transferred to the NARO, Japan, under the Standard Material Transfer Agreement of the International Treaty on Plant Genetic Resources for Food and Agriculture.