Averrhoa bilimbi L. and A. carambola L., Oxalidaceae, are the only two species of the genus Averrhoa L. Their leaves are widely used in folk medicine as an adjuvant in the treatment of diabetes. Some species may contain, for example, calcium oxalate crystals, which may lead to risk in its use when there is predisposition of individuals with reduced renal activity. Therefore, there are still few studies on the content of oxalic acid present in them, highlighting the importance of this investigation. The objective of this work was to conduct a comparative anatomical and histochemical study between the species and determining its content of oxalic acid. Semipermanent histological slides were prepared, following common plant anatomy procedures, for analysis of the leaflets in optical microscopy, polarization and scanning electron microscopy coupled with energy-dispersive X-ray spectrometry. To determine the total, soluble and insoluble oxalate content was used titration with potassium permanganate. The anatomical characterization allowed identifying the characters useful in the differentiation of the species. The histochemistry revealed the location of the metabolites. Chemical microanalyses demonstrated that the crystals are of calcium oxalate. A. carambola presented the highest levels of total oxalate and soluble oxalate. The study assists in the identification and quality control of A. bilimbi and A. carambola and brings new data on its oxalic acid content, which are important, in view of the medicinal use of the species.