— A highly nutritional protein coding gene AmA1 of Amaranthus hypochondriacus was searched in different species of Amaranthus by using various molecular biological techniques. PCR, Southern hybridization, primed in situ labeling (PRINS) and Cycling-primed in situ labeling (C-PRINS) confirmed the presence of AmA1 coding region only in Amaranthus hypochondriacus. The AmA1 gene was successfully localized on interphase nuclei and also on the metaphase chromosomes. The single copy, unique AmA1 gene was found to be present in the subtelomeric region of two homologous chromosomes in the group of 2-2.2 μm in length. In the present study, a rapid and reliable method for physical localization of single gene on plant chromosome was described and both the methods for in situ localization i.e. PRINS and C-PRINS were compared. © 2008 Taylor & Francis Group, LLC.