Grapefruit and lime cutins were analyzed and compared in order to obtain information about their cutin architecture. This was performed using a sequential hydrolysis, first with trifluoroacetic acid to remove most of the polysaccharides present in the cutins, followed by an alkaline hydrolysis in order to obtain the main aliphatic compounds. Analysis by CPMAS 13C NMR and ATR FT-IR of the cutins after 2.0 M TFA revealed that grapefruit cutin has independent aliphatic and polysaccharide domains while in the lime cutin these components could be homogeneously distributed. These observations were in agreement with an AFM analysis of the cutins obtained in the hydrolysis reactions. The main aliphatic compounds were detected and characterized as 16-hydroxy-10-oxo-hexadecanoic acid and 10,16-dihydroxyhexadecanoic acid. These were present in grapefruit cutin at 35.80% and 21.86% and in lime cutin at 20.44% and 40.36% respectively.