During the eukaryote evolutionary history, the acquisition of plastids and the evolution of algae is one of the major transitions that has heavily shaped the earth and its biosphere as it is today. Still, few is known about the ancient endosymbiotic events, the evolution of these algal lineages and the correlation with the earth geological past conditions. One of the main problems, is that we lack molecular data for key extant species with good fossil record, which is fundamental to date the speciation events and help to resolve phylogenetic relationships between extant living species an reconstruct the evolution through the geological time scale. In the current situation of rapid climate change, we need to understand the adaptation and diversification of algae, which are of fundamental ecological importance. We addressed this issue by obtaining molecular data of calcareous algae with a high quality fossil record (Corallinales and Dasycladales) and including them in a plastid-wide phylogenomics study, including all known lineages of Cyanobacteria (the lineage that gave rise to the chloroplast in eukaryotes), the primary algae (Glaucophyta, Rhodophyta and Chloroplastida) and complex algae derived from secondary eukaryotic endosymbiotic events (Haptophyta, Ochrophyta, Cryptophyta, Euglenozoa and Chlorarachnophyta). The results include 2 newly sequenced algal genomes of calcareous red algae including its whole chloroplast genome, a state-of-the-art phylogenomic dataset including over 80 plastid markers (~20,000 amino acid positions) for a wide taxon sampling of more than 300 species, and 10 highly confident calibration points, and a timed tree with narrower time estimates than previous eukaryote-wise studies including diversification rates of each lineage and correlation with paleoclimatic data.