Malaria continues to remain a global health burden. Understanding the molecular mechanisms governing these parasites’ survival is crucial for developing effective interventions. Advances in RNA modification research have unveiled the significance of RNA methylation in gene regulation and pathogenesis. This is the first study to investigate the methylation pattern up to single-base resolution across RNA in clinical samples ofP. falciparumandP. vivaxwith hepatic dysfunction complications using Oxford Nanopore Direct RNA Sequencing. Preliminary findings indicate distinct methylation profiles inP. falciparumandP. vivax, suggesting potential species-specific regulatory mechanisms. These methylation modifications are unevenly distributed across the mRNA’s 3’UTR, CDS, and 5’ UTR, which may influence mRNA export and translation initiation/repression of these primary transcripts. Furthermore, the data provides a glimpse into methylation events in Natural Antisense Transcripts (NATs). The correlation of these layers of regulation will facilitate a comprehensive understanding of the transcriptional environment of malaria parasites.