Contemporary models of the microbial loop should be critically evaluated relative to their compartmental structures, flow networks, and treatment of upper ocean physics (vertical and horizontal boundary conditions). The development of new models that include better representation of the autotrophic components and mixotrophy/competitive interactions is warranted. The mathematical structures should reflect contemporary knowledge of controls (e.g., multiple resource limitation), thresholds and limits, and be based on testable assumptions. Stochastic processes must at some point be included to evaluate known patterns of spatial and temporal variability.