Factors regulating composition and relative abundance in phytoplankton communities were investigated in an ancient lake with a highly endemic food web. Lake Matano has genera diversity (21) similar to tropical lakes, but low phytoplankton biomass (0.0162 µg/L). Vertical mixing physically limits primary production (42% Zeu:Zm); phytoplankton are moved below the euphotic zone. Macronutrient concentrations (0.30 µmol/L N, 0.13 µmol/L P) are low. Nutrient bioassays used N and P (30-320 µmol/L individually, 60:5-1920:160 µmol/L N:P combined). After 16 days, no significant (p > 0.05) changes in relative abundance and no biologically significant changes in phytoplankton biomass occurred. CHU-10 growth media cultivation, however, significantly increased chl-a. Analysis identified lakewater Cr (0.14 µmol/L) above a threshold to restrict algal growth (0.12 µmol/L) and Mo (0.0005 µmol/L) below requirements by most aquatic life (0.008 µmol/L). Therefore, physical (mixing) and chemical (toxicity, micronutrient) factors are concluded to limit composition and relative abundance of phytoplankton in Matano.