The toads Rhinella marina and R. schneideri are large terrestrial true toads widely distributed in the Neotropical region, which can hybridize in areas of transition between Amazon rain forest and Cerrado biomes. The former is in particular an important ecological species, and a very successful invader. Here, we report de novo transcriptome of R. marina and R. schneideri and polymorphism SNPs identified between the two species. The transcriptome sequencing was performed on an Illumina platform using five individuals livers mRNA samples for each specie. A total of 554,474,410 and 554,276,922 sequencing reads were collected and assembled into 199,799 and 172,671 transcripts with N50 lengh of 3106bp and 3106bp for R. marina and R. schnedeiri respectively. A total of 709,193 SNPs were identified and characterize for both species. This transcriptome and SNPs will facilitate studies on hybridization and adaptation of the Rhinella complex but also various ecological and evolutionary studies of other amphibians as few transcriptome data are available.