Acacia mangium, A. auriculiformis, A. crassicarpa and A. mangium X A. auriculiformis hybrid are the most popular Acacia species planted in Southeast Asia for timber and pulpwood production. The ASEAN region has an estimated 2 million hectares of plantations of these tropical Acacia species and there is a growing demand for improved planting materials. The other notable industrial Acacia species is A. mearnsii grown mainly in South Africa (120,000 ha) and Brazil (250,000 ha). Genomic information, such as ESTs, transcriptome sequences, genomic sequences, microRNA sequences and DNA markers has been intensively collected from a limited number of Acacia species mainly to accelerate the breeding process. The accumulating Information will also provide an opportunity to perform comparative analyses to decipher the evolutionary process of genomic structures and functions in leguminous plants. Currently, there are more than 10,000 entries in the NCBI dbEST for A. mangium and A. auriculiformis X A. mangium hybrid. Transcriptomes of A. mangium and A. auriculiformis have been sequenced, assembled and annotated. Some genes involved in wood formation, lignin biosynthesis, shoot and floral development have been identified and characterized. In an attempt to better understand the regulation of lignin genes, the role of small RNAs (microRNAs and siRNAs) which are involved in post-transcriptional gene silencing and epigenetic regulation was investigated. Two small RNAs libraries from samples with contrasting lignin content were generated using Solexa Second Generation Sequencing Technology. Several conserved and novel small RNAs that may serve as an important regulatory sequence during secondary wall formation were identified. Majority of these small RNAs emerged as critical regulators for normal growth and developmental processes. We have validated that a cascade of small RNAs will play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species through real time PCR approach. Resequencing of cinnamoyl coenzyme A reductase (CCR), caffeate O-methyltransferase (COMT), cinnamyl-alcohol dehydrogenase (CAD), cinnamate 4-hydroxylase (C4H) and caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) full length genes enabled the detection of 78 SNPs which were genotyped across 240 individuals of A. mangium and 240 individuals of A. auriculiformis using Illumina Golden Gate Bead Array. Fifteen Single Nucleotide Polymorphisms (SNPs) (six for CCR, three for COMT and six for CAD) were polymorphic in A. auriculiformis whereas eight SNPs (five for CCR, one for COMT and two for CAD) were polymorphic in A. mangium. The paucity of polymorphic gene based SNPs for QTL mapping was addressed by de novo transcriptome assembly using Illumina GAII sequencing. A total of 43,286 putative SNPs were detected from 7,839 contigs assembled from four transcriptomes of parents for two full sib F1 mapping populations (WD and FL). After stringent filtering and validation of a subset of the in silico detected SNPs, a total of 768 SNPs based on two-way pseudo-testcross strategy, even genome coverage and increased assay successful rate were used for linkage analysis. Four linkage maps were constructed for each parent using Joinmap. For WD population, 239 and 163 markers were mapped to paternal and maternal map where 13 linkage groups ranging from 22.9 cM to 156.6 cM were identified. The total lengths of WD paternal and maternal maps were 1086.7 cM and 822.3 cM with an average marker interval of 4.5 and 5.0 cM respectively. For FL population, 78 male and 45 female markers were mapped and total lengths of 498.2 cM and 237.1 cM spanning 10 and 7 linkage groups in male and female parents respectively were obtained. QTL mapping will be carried out after phenotypic evaluation of the mapping populations has been completed in October 2014. This collection of digital transcriptome and small RNA sequences will also provide a wealth of resources for further investigation of genes involved in lignin biosynthesis and wood formation. Better understanding of the structural and regulatory genes involved in the complex lignin biosynthetic pathway and the successful detection of pulpwood quality QTLs in A. mangium, A. auriculiformis and their hybrid will have immediate benefits to the pulp and paper and related industries.