BACKGROUND: The genus Virescentia is a significant member of the Batrachospermaceae, exhibiting distinctive life history characteristics defined by alternating generations. This group of taxa has specific environmental requirements for growth. This paper investigates Virescentia, which primarily thrives in freshwater environments, such as streams and springs, characterized by low light, low temperatures, and high dissolved oxygen levels. Currently, no laboratory simulations of their growth conditions have been reported in culture studies. Additionally, previous studies indicate that comparisons of photosynthetic strength across different life-history stages of the same species have not been conducted, mainly due to the challenges of simultaneously collecting algal strains at both life-history stages. RESULTS: During the gametophyte stage, the chloroplast and mitochondrial genomes were measured at 184,899 bp and 26,867 bp, respectively. In the chantransia stage, the lengths of these genomes were 184,887 bp and 27,014 bp, respectively. A comparison of organellar genome covariation and phylogenetic reconstruction revealed that the chloroplast and mitochondrial genomes across different life history stages were highly conserved, with genetic distances of 0 and nucleotide variants of only 9-15 bp. The mitochondrial genome of gametophyte SXU-YN24005 was found to lack two tRNA-Leu (tag) genes compared to that of the chantransia strain. Additionally, a comparative analysis of KEGG pathway transcriptome data from the two life history stages showed that 33 genes related to the ribosomal pathway and 53 genes associated with the photosynthesis pathway exhibited a significant decline in expression during the gametophyte stage compared to the chantransia stage. CONCLUSION: In this study, two samples of the same species at different life-history stages were collected from the same location for the first time. The analysis revealed a high degree of conservation between their organelle genomes. Additionally, transcriptome sequencing results indicated substantial differences in gene expression patterns between the two life-history stages. This research will provide reliable data to support the future histological database of freshwater red algae and will establish a theoretical basis for conserving rare and endangered species.