Stress-specific expression of cellular proteins in responses to exogenous exposure and resulting physiological alteration provides important insight into the field of ecological research. Due to its habitat, feeding, lifestyle and physiologic properties, mussel has become an important indicative measure of aquatic environment pollution in order to assess effect of these pollution in aquatic life. In order to minimize the threats imposed on the aquatic ecosystem and advancement of sustainable lifestyle for human, recent ecological studies are more concern about monitoring different bioindicative properties. In this study, two widely distributed freshwater bivalve mussel species Anodonta anatina and Unio tumidus was used to conduct comparative study on the transcriptome of these species in order to identify and quantify the expressed transcripts on both species and investigate their biomarker properties in mussels for monitoring heavy metal or toxic exposure. mRNA was isolated and converted to cDNA through reverse transcription PCR. Quality and quantity assessments of purity, fragment size and concentration was performed. Each cDNA sample was barcoded and amplified for cDNA library preparation and nanopore sequencing. Basic bioinformatics tools were used to identify the transcripts for transcriptomic analysis. The findings shows some common mitochondrial and ribosomal transcripts along with a wide range of conserved and abundant transcript variants in mussels with important biomarker properties. Some of the transcripts exhibits expression in multiple samples suggesting characteristic bioindicator properties. Also in this study, a pipeline for transcriptomic analysis was generated and critical steps in the procedure were identified and discussed.