The facts that >75% of marine HABs are caused by dinoflagellates and that ~40% of HABs-causing microalgae are dinoflagellates manifest the vital importance of investigating all aspects of the biology and ecology of dinoflagellates in the international community of HABs research. The life history and its relevant molecular biology are among those of fundamental significance because the switch between vegetative growth and resting stage (cysts) plays a vital role in the HABs dynamics and, more generally, the remarkable adaptive strategies of dinoflagellates. Unfortunately, the molecular processes and functional genes underpinning the dormancy and revival of dinoflagellate cysts had remained to be a completely black box until very recently. Therefore, during the last 8 years we conducted a series of investigations aimed at revealing the genes responding to the life history shift of dinoflagellates, particularly those actively expressed in the resting cysts. Via an approach combining comparative transcriptomics, physiology, and UHPLC-MS/MS and ELISA survey of the resting cysts and vegetative cells of the cosmopolitan HABs-causing species Scrippsiella acuminata, we observed that TCA cycle was still a crucial pathway of energetic metabolism for resting cysts under aerobic condition, especially at the early stage of dormancy, and its expression elevated at higher temperature and light irradiation. The energy consumption of resting cysts reaches a low but somehow stable level within a short time period and is lower at low temperature, darkness, and anoxia than that at ambient condition. We also confirmed a classical plant hormone, abscisic acid (ABA), may play a vital role in regulating encystment and maintenance of dormancy, akin to its function in seed dormancy of higher plants. Via a combined approach of gene cloning, transcriptional detection, e-cDNA library sequencing, and phylogenetic analyses, we found a series of genes encoding heat shock proteins (Hsps), including Hsp70, Hsp60, Hsp10, Hsp40, Hsp90 and sHsps, might function in cyst formation and/or dormancy maintenance. A possibly universal presence of Hsp90s transcripts were also detected in the resting cysts of dinoflagellates buried in marine sediment, which was supported by the abundant transcripts obtained via qPCR for the cold-stored resting cysts of Scrippsiella acuminata in the laboratory. These results collectively raised the possibility that the expression of Hsp genes is part of the machinery maintaining the dormancy or/and the adaptation to ambient conditions of dinoflagellate resting cysts. Our findings together are believed to considerably enhance current understanding of the molecular processes in resting cysts of dinoflagellates.