The oceans of Earth’s middle age, 1.8–0.8 billion years ago, were devoid of animal-like life. According to one hypothesis, the emergence of large, active organisms was restrained by the limited supply of large food particles such as algae. Through the discovery of molecular fossils of the photopigment chlorophyll in 1.1-billion-year-old marine sedimentary rocks, we were able to quantify the abundance of different phototrophs. The nitrogen isotopic values of the fossil pigments showed that the oceans were dominated by cyanobacteria, while larger planktonic algae were scarce. This supports the hypothesis that small cells at the base of the food chain limited the flow of energy to higher trophic levels, potentially retarding the emergence of large and complex life.