Intronic mircroRNAs are a class of miRNAs which locate in intronic regions of any genes. They are short RNAs which are about 18–25 nucleotide long. Similar to the other class of miRNAs, intronic miRNAs have been known as a gene regulator relevant to cell growth and development, and cell response to stresses. According to their significant roles in cellular regulation, experimental as well as computational studies have been performed by aiming at extensive identification of the miRNA in species of interest. However, the finding of intronic miRNA is still limited. In this work, we thus used an ab initio approach to exhaustively search for intronic miRNAs in cassava, a starchy root crop. The study identified 127,485 putative intronic miRNAs partially overlapped with the result of deep sequencing method from the independent study. With the target analysis of these intronic miRNAs, it was suggested that the putative intronic miRNAs are involved in essential cellular activity maintenance and stress response.