Physa acuta (left-handed shell) have strong natural growth activity not only in lentic waters but also in eutrophic environments. Therefore, it has been considered one of the candidate species that could evaluate the degree of water pollution by physiological and biochemical methods. In this study, we constructed a P. acuta cDNA library using the 5′ oligo capping method, and determined the sequences of 2,282 clones by 5′ end-single path sequencing. After trimming, clustering, and assembling these sequences, we finally obtained 575 distinctly available transcripts that were 718 bp in average length. These transcripts were annotated using the BLASTX search and were classified by function using KOG analysis. After comparison with biomarker genes already known in several organisms, we identified 27 potential biomarker candidates that were categorized into two groups strongly related to stress and defense genes by their functions. To the best of our knowledge, this is the first report of massive profiling of cDNA sequences and the characterizing of potential biomarker genes in P. acuta. Our study offers valuable information to scientists for developing new environmental biomonitoring markers, and for scientists studying the physiology, growth and development, immunity, genetic identification, and evolutional diversity in P. acuta.