Haematococcus pluvialis is a green alga known to accumulate astaxanthin in extra-plastidic lipid vesicles under stress conditions. The present study revealed the influence of few cultural parameters and temperature treatments on regeneration efficiency of red cysts along with changes in pigment profile and expression of carotenogenic genes during regeneration. Regeneration efficiency has been improved by incubating less aged cyst cells in a medium containing ammonium carbonate, 16:8 light-dark cycle with a light intensity of 30 mumol m(-2) s(-1). During regeneration, there was a decrease in total astaxanthin, total carotenoids, and carotenoid to chlorophyll ratio, and increase in beta-carotene, lutein, total chlorophyll, and chlorophyll a to b ratio. Expression analysis revealed the presence of transcripts of carotenogenic genes, phytoene synthase (PSY), phytoene desaturase (PDS), lycopene cyclase (LCY), beta-carotene ketolase (BKT), and beta-carotene hydroxylase (CHY) in cyst cells, and these transcripts were up regulated transiently upon transfer to favorable conditions. As the culture growth progressed, carotenogenic gene expressions were decreased and reached basal expression levels of green motile vegetative cells. In addition, this is the first report of detection of carotenogenic gene transcripts in red cysts, and their differential expression during regeneration. The present study suggests the use of red cysts as alternate inoculum for mass cultivation to combat protozoan predation.