Maize (Zea mays L.) is the leading commodity grain crop. Continuous selection for yield has led to the loss of genetic variation for other specific traits that may be important for specialty product end-uses. Blue corn has been of increasing interest for production of specialty products. Little is known about the variation for kernel pigment content of blue corn. Our objective was to assess the anthocyanin content in borderland landraces of maize. In 2012, a total of eight different accessions of blue corn were used in an experimental trial conducted at five different locations across New Mexico and Arizona. Analysis of anthocyanin content was performed on the acidic methanolic extracts of blue corn kernels by UV-VIS spectrometry. Subsequently, the individual anthocyanin constituents were characterized by High Pressure Liquid Chromatography (HPLC). Total anthocyanin content varied from 11.24 to 61.23 mg/100g. The Los Lunas blue accession has shown highest amount of anthocyanin with 61.23 mg/100g and Flor del Rio accession has shown lowest amount of anthocyanin with 11.24 mg/100g. Yoeme blue and Ohio blue accessions have consistently shown higher amounts of anthocyanin, and Flor del Rio has shown the least amount of anthocyanin across locations. Five tentatively-identified anthocyanin peaks were purified and analyzed by high-resolution mass spectrometry. Cyanine-3-Glucoside was confirmed and four other anthocyanins were tentatively assigned elemental compositions.