Many localized vertebrate die offs have been found in the Anembalemba Member in the Maevarano Formation of Northwestern Madagascar during Late Cretaceous (~70 Ma) - microbialites found immediately below the fossil beds suggest seasonal blooms of algae could have introduced toxins into the dry season's shrinking water sources. The ecosystem was a semi-arid floodplain with violent seasonal monsoons - and contained an amazing biodiversity: large theropods, titanosaurs, many crocodiles, and a number of birds and mammals. Biomarkers, the degradation products of cell membrane lipids, preserved in the rocks offer a glimpse into the microbial ecology of this system. By using evidence from paleontology, organic geochemistry, and comparisons with similar ecosystems in modern-day Sub-Saharan Africa, the seasonal cycles in the basin can possibly be outlined and importantly when toxic algal blooms may have happened. The Anembalemba Member’s yearly climate, like many subtropical semi-arid ecosystems, alternated between dry seasons and monsoon seasons. During the dry season the river dried up and microbial mats formed in the remaining ponds. As rains started to return, nutrient pulses carried by upstream water and by wildlife might have created conditions perfect for photosynthetic algae and cyanobacteria, but significantly toxin-producing dinoflagellates and to a lesser extent cyanobacteria could have bloomed - as animals drank from the potentially poisoned water they died and were left to decompose on the dry floodplain. Once monsoon season was in full swing, violent floods swept up the often articulated animal remains and deposited them in a poorly-sorted sandstone. To justify the harmful algal bloom (HAB) cycle, the biomarkers of dinoflagellates and cyanobacteria were found to change in a similar pattern to known modern blooms in analogous ecosystems. The Maevarano Formation may contain some of the oldest documented HAB events, and organic geochemistry can help shed light on the nuanced paleoecology of Late Cretaceous Madagascar.