Dwarf or short palm is considered one of the desired traits in oil palm breeding, offering advantages of extending the economic viability and harvesting. This study aimed to identify single nucleotide polymorphism (SNP) markers associated with height increment (Hinc) for future breeding improvement programmes. A total of 537 SNPs and 107 Elmina x Ulu Remis (ELxUR) hybrid palm crosses were used in the marker-trait association study, with phenotypic data collected at age 8 and 16. Eight significant SNPs were detected associated with Hinc on chromosome 1, 2, 3, 4 and 10. Candidate gene identification within these significant SNPs was performed using the palm genome sequence and bioinformatics tools, revealing 13 potential candidate genes and transcription factors linked to phytohormone biosynthesis, signalling and plant growth. This study provides a groundwork for implementing marker-assisted breeding for the height trait within the ELxUR oil palm breeding materials.