The mechanically induced molecular deformation of cellulose nanowhiskers embedded in subpercolation concentration in an epoxy resin matrix was monitored through Raman spectroscopy. Cellulose nanowhiskers isolated by sulfuric acid hydrolysis from tunicates and by sulfuric acid hydrolysis and hydrochloric acid hydrolysis from cotton were used to study how the aspect ratio (ca. 76 for tunicate and 19 for cotton) and surface charges (38 and 85 mmol SO4 (-)/kg for sulfuric acid hydrolysis of cotton and tunicate, respectively; no detectable surface charges for hydrochloric acid hydrolysis) originating from the isolation process influence stress transfer in such systems. Atomic force microscopy confirmed that uncharged cellulose nanowhiskers produced by hydrochloric acid hydrolysis have a much higher tendency to aggregate than the charged cotton or tunicate nanowhiskers. Each of these nanowhisker types was incorporated in a concentration of 0.7 vol % in a thermosetting epoxy resin matrix. Mechanically induced shifts of the Raman peak initially located at 1095 cm(-1) were used to express the level of deformation imparted to the nanowhiskers embedded in the resin. Much larger shifts of the diagnostic Raman band were observed for nanocomposites with tunicate nanowhiskers than for the corresponding samples comprising cotton nanowhiskers. In the case of nanocomposites comprising nanowhiskers produced by hydrochloric acid hydrolysis, no significant Raman band shift was observed. These results are indicative of different modes of stress transfer, which in turn appear to originate from the different sample morphologies.