In this study, the antifungal activities of cinnamaldehyde and eugenol congeners against white-rot fungus Lenzites betulina and brown-rot fungus Laetiporus sulphureus were evaluated and the relationships between the antifungal activity and the chemical structures were also examined. Results from antifungal tests revealed that cinnamaldehyde, alpha-methyl cinnamaldehyde, (E)-2-methylcinnamic acid, eugenol and isoeugenol exhibited strong antifungal activity against all fungi tested. Results derived from the chemical structure-antifungal activity relationship study suggested that compounds with an aldehyde group or an acid group, a conjugated double bond and a length of CH chain outside the ring affect their antifungal properties. Furthermore, the presence of the methyl moiety in the ortho position may have a considerable influence on the inhibitory action against L. betulina and L. sulphureus. In addition, the lipophilicity may play, in part, a crucial role in determining the toxicity of phenylpropenes.