El Japón is a 16th century hamlet site in the marshlands of the southern Basin of Mexico in central Mesoamerica. Radiocarbon (14C) dating and OxCal modeling of human bone collagen (n = 11) identifies a range of burials at El Japón cemetery from 1550–1650 cal. CE. The refined chronology identifies use of this rural settlement well after the onset of colonial government-sponsored relocation of Indigenous people to larger settlements (congregaciones). Historically documented information in this work supports chronological modeling beyond stand-alone calibration. Stable isotopic study of bone samples demonstrates similar sources of dietary protein and carbohydrates. The similarity of carbon sources for bone apatite (bioapatite) and collagen offers security that both bone fractions are viable 14C dating opportunities. Recent extension of this work examines bioapatite 14C dates (n = 5) from the same bone samples when quality parameters are met—atomic carbon-nitrogen ratios of 3.2–3.3 and collagen yield of 10–20%. No significant difference is found between collagen and bioapatite dates of the same individuals (p = 0.17, Mann-Whitney U test). 14C dates from human bone samples in this primarily terrestrial dietary context can be successfully acquired from either collagen or bioapatite fractions.