Fungi, are responsible for large post-harvest losses in various commodities. In particular, Penicillium digitatum, which is responsible for up to 90% of the total losses to the Brazilian citrus crop in the post-harvest period. During infection in the citrus host, the phytopathogen P.digitatum synthesizes tryptoquialanines A and C alkaloids in vivo, which could represent a problem for the world population, since mycotoxins produced by fungi in general are notoriously toxic. The objective of this project were to isolate, characterize and develop and validate an analytical method to determination of tryptoquialanines A and C during the infection of the fungus P.digitatum in orange (layers: epicarp, mesocarp and endocarp), evaluating the level of diffusion of these mycotoxins in different stages of infection. Purification of the standards was performed by chromatographic techniques and the compounds were characterized by NMR ( 1 H, 13 C, HSQC, HMBC) and Liquid Chromatographic coupled to High Resolution Mass Spectrometry (LC-HR-MS) techniques. The purified alkaloid standards were then used to develop and validate the analytical method which employed the QuEChERS extraction method, modified with the aid of experimental planning and the quantification of the analytes was carried out by Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS). The linearity obtained was 5 -400 μg/kg with r > 0.99 for tryptoquialanines A and C. The limits of detection (LOD) and quantification (LOQ) were 5 μg/kg and 10 μg/kg, with the exception of the TC compound in the epicarp extract, where the LQ was 25 μg/kg. The recoveries between 58 and 101%, with relative standard deviations (RSDs) ≤ 12% showed the accuracy of the method. The presence of the tryptoquialanines A and C was observed in different levels of infection of the orange, showing the diffusion of the metabolites occurs only from the intermediate stage of the infection.In addition, the presence of the compounds in the epicarp layer (blank), which was in direct contact for 48 hours with infected orange, showed the contamination process among oranges by the alkaloids, after this exposure period. Tryptoquialanines compounds A and C did not demonstrate antiproliferative and cytotoxicity abilities in the tests performed (HeLa, HUVEC and K-562), which suggests absence of activities for the analyzed cells.