Elaeis guineensis is a tropical oil plant with the highest oil yield per unit area in the world. The Tenera hybrid is the most valuable variety for cultivation compared to the parent varieties Dura and Pisifera. It is difficult to select for the morphological characteristics of the oil palm cultivar in oil palm seedlings at the nursery stage; thus, the development of a molecular marker is necessary. In the present study, a sequence characterized amplified region (SCAR) marker was developed that yields 159-bp and 195-bp fragments specific for female and male parents, respectively. Sequence alignment revealed that the 159-bp fragment has a 36-bp deletion. Molecular characterization of the fragments reveals that the sequence is identical to the ALBINO3-like protein 2 (EgALB3.2) and is localized on chromosome 16 of the E. guineensis genome with expression noted in the kernel/endosperm of Tenera fruits only. These markers help in the selection of oil palm hybrids codominantly expressing both fragments; thus, heterozygous individuals can be distinguished from homozygous individuals. The SCAR-specific marker could therefore be used to distinguish oil palm hybrids from their parents by PCR. Moreover, these specific SCAR primers can be used directly to identify the oil palm hybrids without the need for postprocessing steps, and the specific fragments can be detected using an automated sequencer and real-time PCR. This marker-assisted selection is sensitive and suitable for the identification of oil palms in breeding programs.