Eucalyptus is an important source of cellulose and a widely cultivated plant. Biotechnology tools can save time spent in breeding and transcriptomic approaches generate a gene profile that allows the identification of candidates involved in processes of interest. RNA-seq is a commonly used technology for transcript analysis and it provides an overview of regulatory pathways. Here, we selected two contrasting Eucalyptus species for cold acclimatization and focused in responsive genes under cold condition aiming woody properties – lignin and cellulose. The number of differentially expressed genes identified in stem sections were 3.300 in Eucalyptus globulus and 1370 in Eucalyptus urograndis . We listed genes with expression higher than 10 times including NAC , MYB and DUF family members. The GO analysis indicates increased oxidative process for E. urograndis . This data can provide information for more detailed analyses for breeding, especially in perennial plants.