Carbonate rocks play an important role in petroleum geology by acting as reservoir rocks, generators, and even hydrocarbon sealants, accounting for about half of the oil and gas reserves known in the world. The study of these carbonate rocks have become very important in the hydrocarbon exploration scene in Brazil because of they consist in analogous for reservoir rocks of the presalt interval. Thus, the objective of this research was to use X‐ray microfluorescence (micro‐XRF) and X‐ray microtomography analysis, as complementary techniques, in order to characterize samples of carbonate rocks in respect to their structures, textures, mineralogy, and pores. The microtomographic analyses allowed the identification of the horizontal structures as parallel lamination, horizontal, and vertical fractures filled by calcite and biotic constituents (gastropods bioclasts). Different composition of minerals were also identified, as calcite, quartz, feldspars, iron sulfides, and oxides. The porosity (ranges <1 to17%), and the high‐density elements could also be quantified, as well as their distribution in each sample. The micro‐XRF analysis present a direct relationship with the distribution of minerals that compound carbonate rocks, highlighting some structures, as well as helping to identify trace and minor elements in the carbonates (Mn, Sr, and Mg).