||Identification of the RNA targets of any RNA-binding protein (RBP) is essential for complete understanding of understanding of its biological functions. However, it is still a challenge to identify those biologically relevant targets of RBPs through in vitro strategies RIP-seq, HITS-CLIP, or GoldCLIP due to the potentially high background and complicated manipulation. In the human malaria parasite Plasmodium falciparum, RIP or gene disruption are the few tools available currently for identification of RBP targets. Here, we have adopted the TRIBE (Targets of RNA binding proteins identified by editing) system to identify the RNA targets of PfDis3, a key exoribonuclease subunit of RNA exosome in vivo. By stranded RNA sequencing of a transgenic parasite line of Pfdis3-ADARcd, which catalyzes an adenosine (A)-to-inosine (I) conversion corresponding to those potential interacting sites of PfDis3-targeting RNAs, we have found that approximately 40.2% (2250/5602) genes in the nuclear genome were targeted by PfDis3 for sense transcripts and 27.4% (1534/5602) genes for antisense transcripts, which are involved in multiple biological processes in the IDC. Furthermore, comparative analysis of the targeting genes identified by TRIBE, RIP-seq, and Pfdis3 gene knock down showed that a significant proportion of PfDis3-ADAR-edited genes were not identified by the routine assays, suggesting a higher sensitivity of TRIBE in identification of protein-binding RNAs. Overall, by developing the TRIBE technique in P. falciparum, we have demonstrated that PfDis3 shapes the dynamic transcriptional transcriptome of malaria parasites through post-transcriptional degradation of a variety of unwanted transcripts from both strands throughout the IDC.