Capsaicins, hot principles in Capsicum spp., are produced from vanillylamine and short-chain fatty acids (FAs), originated from branched amino acids. Recently a minor but clear incorporation of longer chain FAs with 14-18 carbons to novel long-chain vanillylamides was reported, which prompted further investigation on possible correlation between metabolism of capsaicins and FA precursors with metabolite profiling. Placenta of Capsicum annuum with different concentrations of capsaicins were extracted and analyzed with gas chromatography-mass spectrometry. Structures of FAs were determined after derivatization to methyl- and picolinyl esters. The results indicate cultivars with more capsaicins contain higher amount of long-chain branched FAs with 14-17 carbons. Some branched FAs showed strong correlation with the level of capsaicins. Most branched FAs are of iso-acids, where the methyl groups are attached at (${omega}$-1) carbon, whereas only one anteiso-FA was observed in a single cultivar. In addition to saturated analogues, several mono-unsaturated branched FAs have also been detected. Location of double bond in these metabolites suggested that short-chain branched FAs may be incorporated in the middle of biosynthesis or at initial steps of long-chain FAs. Accordingly, branched medium- to long-chain FA may be derived mainly from leucine or valine, rather than isoleucine. Results indicate that the short-chain FAs are possible precursors both of capsaicins and methyl-branched longer chain FAs.