Hydroxyapatite in tooth enamel uptakes several elements while in burial environment (diagenesis), which alters the chemical composition and consequently the life history reconstruction. Fourier Transform Infrared Spectroscopy (FTIR) is used in this study to evaluate the diagenesis of hydroxyapatite by measuring the peaks of phosphate and francolite vibrations. The study comprises 28 teeth from the sites of Ya’amun (MBA) and Yasieleh (B) in northern Jordan, dated to the Middle Bronze Age (MBA) and the Byzantine (B) period respectively. The FTIR results showed that all of samples contained calcite and fluorine, and thus, point to soil-tooth exchange after decomposition. The average values of Crystallinity Index in the tombs of Ya’amun (MBA) and Yasieleh(B) signify minimal if any diagenesis, significance level of the test is ? = 0.05. The analysis of variance on the francolite absorbance values shows that the mean value of francolite absorbance among the two sites is different and consequently varied tomb use chronologies, which was shorter at Yasieleh(B). The results conclude that the short deposition time at the site of Yasieleh (B) is a clear indication of massive deaths caused probably by an epidemic disease