The bottom fraction of the latex from the Brazilian rubber tree (Hevea brasiliensis), specifically the biological membranes that includes lutoids and the Frey-Wyssling complex, may undergo changes in its membrane lipids and membrane proteins. The changes could affect the coagulation rate of the latex during the tapping process and the speed of blockage of the incision of the latex vessels, thereby preventing the flow of latex and reducing yield. Two types of rubber trees with rapid and normal coagulation rates of latex were selected. Liquid chromatography-mass spectrometry technology (with both positive and negative ion detection modes) was used to qualitatively and quantitatively analyze the lipids in the bottom fraction of the two types of latex, obtaining information on differential lipids. In the bottom fraction of the latex from trees with normal coagulation rates, phosphatidylethanolamine was the most abundant phospholipid subclass (accounting for about 22% of total lipids in negative ion mode and about 5.9% in positive ion mode); it was greater than phosphatidylcholine (about 12% in positive ion mode and about 4% in negative ion mode); phosphatidic acid had a high abundance (about 4% in positive ion mode and about 12% in negative ion mode), comparable to phosphatidylcholine; cardiolipin was abundant in the bottom fraction (about 6% in negative ion mode) and may be present in the Frey-Wyssling complex. In the rubber trees prone to rapid coagulation, cardiolipin in the bottom fraction significantly decreased to about 3.4% in negative ion mode. The phospholipids in the bottom fraction accounted for 31%-56%, neutral lipids 35%-54%, and glycolipids only 1%-2%. The bottom fraction contained a high abundance and quantity of non-bilayer phospholipids, namely phosphatidylethanolamine, phosphatidic acid, and cardiolipin, showing a highly dynamic nature of the latex bottom fraction. The significant downregulation of cardiolipin in the latex prone to rapid coagulation may affect the stability of the bottom fraction, thereby affecting latex coagulation, laticifer blockage, and latex flow. The discovery of high abundant non-bilayer phospholipids in bottom fraction in this study introduces a new perspective into the research of latex coagulation and laticifer blockage mechanisms.