Proanthocyanidins (PAs) are a set of important phytochemical compounds in Lycium ruthenicum Murr. However, PA biosynthesis in L. ruthenicum remains unclear. In this study, leucoanthocyanidin reductase (LAR) and anthocyanidin reductases (ANR) involved in PA biosynthesis wereretrieved from L. ruthenicum EST database. Polymerase chain reaction (PCR) results confirmed that LrLAR and LrANR encoded a protein composed of 333 and 338 amino acids, respectively. Phylogenetic analysis showed that LrLAR and LrANR were clustered with known LAR and ANR proteins of other plants, respectively. Quantitative reverse-transcription PCR (qRT-PCR) results indicated that both genes expressed in a sharp increase manner from unripe stage to color break stage and were down-regulated increasingly hereafter, and that both expression levels are extremely low in young leaves, mature leaves, stems, and roots compared with fruits. Phytochemical assay revealed that the content of total PA in fruit was higher than that in young leaves, mature leaves, stems, and roots, and that the total PA level was increased sharply and then relatively stable hereafter during fruit ripening. Our results lay a foundation for uncovering the PA biosynthesis and further engineering manipulation in L. ruthenicum.