A genome-wide association Study (GWAS) detects linkages between markers and traits of interest for application in genomics-guided breeding. This study utilized GWAS to identify quantitative trait loci (QTL) associated with important agronomic traits in selected palms from Malaysian Palm Oil Board’s (MPOB) African germplasm collection. A total of 635 African oil palm accessions from Angola, Madagascar, Nigeria, and Tanzania were genotyped using a 4451 Single Nucleotide Polymorphism (SNP) Chip via the Illumina platform. Subsequently, genetic diversity was analyzed using 1464 informative SNP markers, and the Angola germplasm was discovered to have the highest heterozygosity and, as expected, Madagascar the lowest. Population structure analysis revealed two main subpopulations, Madagascar versus the others (Angola, Nigeria, and Tanzania). Linkage disequilibrium (LD) analysis conducted using Haploview 4.2 suggested LD decay to be 1.9 kb at r2 = 0.1. Based on fixed and random model calculating probability unification (FarmCPU) analyses, 49 markers were significantly associated with 17 phenotypic traits, some located within the genomic regions associated with similar traits in other studies. QTL on chromosomes 6, 9, and 11 are common among the germplasm and advanced populations, thereby suggesting that the genomic region is selectively fixed in advanced breeding lines. This adds confidence to their potential utility in breeding programs to enhance selection efficiency and progress of the genetic improvement of a perennial crop like oil palm. Interestingly, protein STRUBBELIG-RECEPTOR family 6 and Beta-galactosidase 11 genes were also observed in the QTL intervals, which are potential candidates in expression studies to further dissect the genetic architecture of the traits.