Osmopriming of seeds can increase seed vigour, allowing faster germination and field emergence, especially under adverse field conditions. The restricted imbibition during priming treatments reactivates metabolism although germination will be prevented. In order to identify and characterize genes that are involved in the improvement of vigour of Poincianella pyramidalis (Catingueira) seeds upon priming, we produced two different Suppression Subtractive Hybridization (SSH) cDNA libraries. These were a Forward and Reverse subtraction of cDNA samples isolated from untreated dry seeds (unprimed) and osmoprimed seeds. The two different libraries were sequenced by Illumina GAII next generation sequencing, resulting in almost 20 million reads that could be assigned to 5298 different contigs. Of these, 999 were only found in the unprimed seeds library and 2711 were specific for osmoprimed seeds. The contigs were annotated and subjected to gene set enrichment analysis and differential expression of several genes was confirmed by qRT-PCR analysis. The identified differentially expressed genes might play an important role in vigour improvement upon priming and may be potential markers for tolerance to water stress in P. pyramidalis seeds.