Autofluorescence of plant tissues can be used as a label-free method to detect a range of phenolic-based cell wall components including lignin, suberin, and ferulate using widefield or confocal fluorescence microscopy. Likewise, fluorescently labeled antibodies can be used to localize specific carbohydrate molecules including arabinoxylan, β-1,4 galactan, glucomannan, glucuronoxylan, pectins, and xyloglucan. When combined, these two methods allow detailed study of topochemistry in different plant tissues for phenotyping of mutant varieties and plant biology studies. This article describes the protocols for fluorescent detection and imaging of molecules in plant cell walls using autofluorescence and immunofluorescence.