The mesocarp of oil palm fruit, which constitutes 45%-55% oil by weight, is the primary source of oil, and its quality directly impacts economic value. High lipase activity in the mesocarp raises free fatty acid (FFA) levels, which serve as critical indicators of oil quality. This study aimed to screen IOI oil palm materials with low acidity levels using three published SSR markers. Two markers, mEgCIR_ LIP07 and DelEgCIR_C1E3, showed no polymorphism in four breeding crosses, while mEgCIR_LIP03 showed polymorphism only in the Ulu Remis Tenera (URT) cross. DNA sequencing of mEgCIR_LIP03 revealed two alleles: (TG)₆ (TA)₇ (281 bp) and (TG)₀ (TA)₂₉ (325 bp). The marker-trait correlation study showed a clear trend: The single marker allele (281 bp) was predominantly associated with lower FFA values, while the combined presence of two alleles (281 and 325 bp) or the single 325 bp allele was skewed towards higher FFA values. By using the mEgCIR_LIP03 marker, we can eliminate high lipase palms, allowing breeders to identify potential low lipase palms and develop an elite low lipase line of URT.