The 26 December 2004 tsunami covered significant portion of a coastal zone with a blanket of potentially contaminated sediments. In this report are presented results on mercury concentrations in sediments deposited by the tsunami in a coastal zone of Thailand. Since the total mercury concentrations are insufficient to assess mercury mobility and bioavailability in sediment, its fractionation was applied. Sediments were sampled within 50 days after the event and analyzed by sequential extraction method. The procedure of sequential extraction involved five subsequent stages performed with solutions of chloroform, deionized water, 0.5 M HCl, 0.2 M NaOH, and aqua regia. The mean concentration of total mercury in sediments was 119 ± 50 ng g−1 dry mass (range 66–230). The fractionation revealed that mercury is mainly bound to the least bioavailable sulphides 75 ± 6% (range 62–86), organomercury compounds 14 ± 7% (range 4–26), and humic matter 9 ± 7% (range 1–27). The lowest contributions bring fractions of water-soluble mercury 0.8 ± 1.0% (range 0.1–3.6) and acid soluble mercury 0.9 ± 0.5% (range 0.2–2.1). Although, the total mercury content is similar in a reference sample and in the tsunami sediments, the highly toxic organomercury fraction contribution is higher in the latter. The results were compared with chemical and sedimentological properties of the sediments but no significant correlations were obtained between them.