Abstract: This study examined DNA sequence variations of coding regions of Cinnamate 4-hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) in Acacia mangium and A. auriculiformis. cDNA fragments of C4H and CAD with size 1.5 and 1.3 kb, respectively were cloned into pGEM-T Easy Vector and were sequenced. Twenty eight Single Nucleotide Polymorphisms (SNPs) were identified in the coding region of C4H of which 8 caused changes in the amino acids or nonsynonymous mutations and 20 were synonymous mutations. Thirty two SNPs were detected in coding region of CAD. Of these, 12 were nonsynonymous mutations and 20 were synonymous mutations. Two A. mangium individuals (M20 and M22) and two A. auriculiformis individuals (A6 and A3) were used as parents for generating F1 mapping populations. Nucleotide sequence alignment of coding region of CAD detected 28 and 22 SNPs from A3xM22 parental combination and A6xM20 parental combination respectively. Nucleotide sequence alignment of coding region of C4H identified 6 and 23 SNPs for A3xM22 and A6xM20 parental combinations, respectively. For parental combination A3xM22, 11 nonsynonymous mutations were detected while for A6xM20 parental combination 23 nonsynonymous mutations were detected from CAD gene. Amino acid sequence alignment of C4H detected 4 amino acid variations from each parental combination. The putative SNPs can be developed as SNPs markers for Quantitative Trait Loci (QTL) detection. Selecting favourable alleles from progenies which produce desirable lignin profiles would be advantageous in tree breeding programmes for plantation establishment.