The early development stages of the frog Xenopus laevis are known as the regenerative (R) stage, because during that time, it is able to regenerate. After its metamorphosis into a frog, X. laevis goes into its non-regenerative (NR) stage. It has been reported that there are differences in the gene repertoire expressed at each stage after spinal cord injury, and also in its timing. One molecular agent that might influence gene expression and its timing are small non-coding RNAs (snc-RNAs). To gain insights into the role of snc-RNAs, in this work we aimed to investigate their differential expression between the R and the NR stages and their origins in genome regions. We have performed small RNA sequencing and differential expression analysis between the R and the NR stages. The majority of sequenced snc-RNAs have high quality, and their lengths suggest that the majority belong to the small interfering or, to the micro RNA class. In average, 98% of the ~50 million sequences completely aligned to X. laevis genome, and ~45% of them represent novel snc-RNAs. The snc-RNAs were further classified in 2.238 families, using as criteria their genomic location: ~49% of novel snc-RNA are in TEs regions. ~53% of families have their origins in genes (~33% in intronic regions) and ~47% in intergenic regions. 374 novel snc-RNAs are differentially expressed. 289 come from TEs, 250 of which are in intergenic regions and 39 are in intronic regions. These results, taken together with the differentially expressed genes, will help understanding the spinal cord regeneration process in frogs.