Molecular species of acylglycerols (AG) in the lipid extracts of guayule (Parthenium argentatum) and Hevea (Hevea brasiliensis) rubber particles were compared using HPLC and MS. The contents of 54 molecular species of AG in the lipid extract of guayule rubber particles in decreasing order were as: LLnLn (4.6%), LLLn (3.6%), LLn-OH20:0 (2.4%), LnLnLn (1.9%), LLnP (1.3%), LLP (1.3%), LLn-OH20:1 (0.80%), LLL (0.62%), total of about 24%. The normal FA among the total FA was about 88%, hydroxy FA about 12% and odd carbon-numbered FA about 2.4%. The contents of 56 molecular species of AG in the lipid extract of Hevea rubber particle were as: 308-308-308 (21%), 308-308-O (4.9%), 308-308-324 (4.3%), 308-308-S (2.8%), 308-308-L (2.4%), 308-OL (1.5%) and LLL (1.3%), total of about 44%. 308 and 324 were the furan FA with the masses of 308 and 324. Furan FA with the mass 308 was 10,13-epoxy-11-methyloctadeca-10,12-dienoic acid identified earlier. We proposed the structure of 324 as 10,13-epoxy-11-carboxyl-12-methyl-hexadeca-10,12-dienoic acid. Furan FA among the total FA was about 81%, normal FA about 17% and hydroxy FA about 1.6%. This is the first report of various intact molecular species of AG in rubber particles. It is also the first report of hydroxy FA in the neutral lipids in either species. The major FA in the total FA of guayule were L (38%), Ln (38%), in Hevea was 308 (76%). The molecular species of AG profiles of guayule and Hevea rubber particles may provide the necessary information to further improve guayule and Hevea natural rubbers.