Phosphoglycerate-mutase (PGM) is an ubiquitous glycolytic enzyme, which in eukaryotic cells can be found in different compartments. In prokaryotic cells, several PGMs are annotated/localized in one compartment. The identification and functional characterization of PGMs in prokaryotes is therefore important for better understanding of metabolic regulation. Here we introduce a method, based on a multi-level kinetic model of the primary carbon metabolism in cyanobacterium Synechococcus elongatus PCC 7942, that allows the identification of a specific function for a particular PGM. The strategy employs multiple parameter estimation runs in high CO2, combined with simulations testing a broad range of kinetic parameters against the changes in transcript levels of annotated PGMs. Simulations are evaluated for a match in metabolic level in low CO2, to reveal trends that can be linked to the function of a particular PGM. A one-isoenzyme scenario shows that PGM2 is a major regulator of glycolysis, while PGM1 and PGM4 make the system robust against environmental changes. Strikingly, combining two PGMs with reverse transcriptional regulation allows both features. A conclusion arising from our analysis is that a two-enzyme PGM system is required to regulate the flux between glycolysis and the Calvin-Benson cycle, while an additional PGM increases the robustness of the system.