We have developed new methods for high-throughput RNA and DNA sequencing based on the use of thermostable group II intron-encoded reverse transcriptases (TGIRTs). TGIRT enzymes have higher fidelity and processivity than commonly used retroviral reverse transcriptases, along with a novel template-switching activity that enables attachment of sequencing adapters to nucleic acid template sequences without tailing or RNA ligation. The latter activity enables RNA-seq library construction from small amounts of degraded RNA samples, such as FFPE tumor slices or cell-free (cf) RNAs in human plasma, in <2 h. Validation of the method using fragmented human reference RNAs with ERCC spike-ins demonstrated advantages compared to the widely used TruSeq v3 method, including higher strand-specificity, more uniform 5’- to 3’-gene coverage, and detection of more splice junctions, particularly near the 5’ ends of genes, even from fragmented RNAs. Importantly, TGIRT-seq enables the quantitative profiling of small non-coding (nc) RNAs in the same RNA-seq as protein-coding and long ncRNAs and gives full-length, end-to-end reads of tRNAs and other structured small ncRNAs, neither of which is possible with other RNA-seq methods. TGIRT-seq of cfRNAs in human plasma revealed RNA fragments derived from protein-coding genes and lincRNAs, as well as tRNAs, Y RNAs and most other classes of structured small ncRNAs, with many tRNAs being full-length transcripts rather than fragments as reported previously. In a separate study, TGIRT-seq of RNAs present in highly purified HEK-239T cell exosomes in collaboration with the Schekman lab (UC Berkeley) showed that the predominant membrane-encapsulated RNA cargos are full-length tRNAs and other small ncRNAs, along with smaller amounts of spliced mRNAs, which can vary with cell type. Finally, TGIRT single-stranded (ss) DNA-seq of cell-free DNA in human plasma enabled analysis of (i) nucleosome positioning, (ii) transcription factor occupancy, (iii) DNA methylation sites, and (iv) tissues-of-origins comparably to conventional ssDNA-seq methods, but with a more streamlined workflow that enables precise mapping of DNA ends. Current efforts focus on the use of TGIRT-seq for analysis of patient primary tumor tissues, PBMCs, and plasma samples for diagnostic applications.