Sweetpotato (Ipomoea batatas L), the herbaceous plant cultivated for its starchy storage roots, has a complex genome (2n = 6x = 90) with the estimated genome size of about 4.5 GB. Albinism, a phenomenon that occurs in plants, is defined as the total pigment loss accompanying with insufficient chloroplast membrane differentiation. For this study, an identified natural albino mutant of Xuzi-8 cultivar was subject to RNA sequencing relative to the green plants of identical cultivar. The results showed that total chlorophyll, chlorophyll a, chlorophyll b, and carotenoids were significantly lower in albino plants than in normal green plants. In addition, the CO2 assimilation rate, intercellular CO2 concentration, conductance level, and transpiration rate were significantly higher in normal green plants than in albino mutants. High-quality reads in the total number of 27,520,273-39,862,794 were obtained following the removal of the potentially contaminated or low-quality reads from the albino-mutant and normal green sweetpotato libraries. Later, sequences were matched with the available online data of Ipomoea batatas, and a very low matching degree (2.22%) was obtained, which indicated the very few available data of Ipomoea batatas genome compared with other plants. Additionally, the obtained unigenes were conducted functional annotations and classification, including GO, KOG, and KEGG analyses. The significance level and DEGs differences