A simple and efficient protocol is reported for the isolation of RNA from embryos and leaves of pecan [Carya illinoinensis (Wangenh.) K. Koch]. The method relies on suppression of the polyphenols from interaction with the RNA and their rapid removal from the homogenate by chloroform extraction. This method produced abundant amounts of high-quality RNA. This protocol is likely to be useful for Juglandaceous species and other recalcitrant plants with high levels of phenolic compounds.