Small RNAs (sRNAs), such as microRNAs, have important regulatory roles in both plants and animals despite their short sequences. While the biogenesis pathways of some small RNAs is clear, for other regulatory sRNAs, like tRNA-derived sRNAs, it is less clear in plants. Now it is becoming clear that many diverse cellular RNAs in plants have post-transcriptional RNA modifications and their function is only starting to be elucidated. Here we address the question whether two RNA modifications, N6-methyladensoine (m6A) and 5-methylcytosine (m5C), play a role in sRNA biogenesis in Arabidopsis thaliana. To answer this question, we Illumina-sequenced sRNAs from wild type and the m6A and m5C methyltransferase mutants mta and trm4b, respectively. Our bioinformatics analysis identified 163 sRNA loci that were increased in abundance and 11 sRNA loci that were decreased in abundance in the mutants when compared to the wild type control. Interestingly, we identified 154 sRNA loci produced only in trm4b and this suggests m5C may protect long precursor RNAs from subsequent RNA processing. We are currently characterizing a candidate ribonuclease that may cleave m5C depleted RNAs. In summary, our results suggest that RNA modifications do contribute to sRNA biogenesis in Arabidopsis thaliana.