The aim of this work was to develop a new method to determine the mercury (Hg) concentrations in phosphate rock using a dedicated analytical instrument (the DMA80 Tricell by Milestone) that employs an integrated sequence of thermal decomposition followed by catalyst conversion, amalgamation and atomic absorption spectrophotometry. However, this instrument underestimates Hg concentrations when phosphorite and apatite rocks are investigated with a classic thermal decomposition treatment that complies with US EPA method 7473. Therefore, to improve the recovery of total Hg, we performed alkaline fusion digestion (AFD) directly inside the furnace of the instrument, using BCR(32) as a certified reference material (Moroccan phosphate rock--phosphorite). The salts used for the AFD were a mixture of Na2CO3, K2CO3 and Li2CO3, which melt at about 400°C, due to their ability to form a ternary eutectic and to decompose the phosphorite matrices at 700°C. By adopting this analytical approach, the Hg recovery in BCR(32) was about 100%, compared to 40% when the reference material was analysed without using the alkaline fusion salt. We suggest that the AFD allowed the decomposition of the sample matrix and that some Hg compounds linked with other functional groups may be transformed in carbonates that sublimate at lower temperatures than other Hg compounds. This original method was tested on a number of different geological samples to compare the differences between the AFD method and the thermal treatment in order to verify the working range and to check the robustness of the new approach.