The European Commission manages fish stocks by applying a fishing mortality based on the maximum sustainable yield concept. So far most Baltic Sea fishing maximum sustainable yieldmodels have focused on one species at a time. The few existing multi-species models have assumed that a species’ maturity and growth is dependent on the availability of food. Our two-species models make it possible to investigate if there is a conflict between fishing maximum sustainable yield for cod and herring in the Baltic Sea. This two-species model of cod, as a predator and herring as prey, takes into account environmental drivers on cod and herring recruitment. Reproductive volume together with year-growth, (a year specific effect on growth of external variables like food availability) and predation by grey seals was included in the cod model. The herring model was dependent on cod spawning stock biomass and year-growth. The result shows that the reproductive volume is the main factor that affects the maximum sustainable yield for cod. The spawning stock biomass at maximum sustainable yield is more sensitive to reproductive volume than year-growth. When predation from seals is added in mortality and high environmental factors occurs the spawning stock biomass would be 50% compared to the spawning stock biomass at high environmental effects without seal predation. Four simulations of high cod spawning stock biomass were devastating for the herring population that was eradicated with high predation pressure. The herring maximum sustainable yield depends on the amount of cod spawning stack biomass i.e. the effect of high or low reproductive volume. Two analyses were made on a current environmental state for both species. The first analysis had a natural mortality of 0.2 for cod, which gave an fishing mortality of 0.20 and maximum sustainable yield of 410 000 tons. The herring had a fishing mortality of 0.03 and maximum sustainable yield of 11 000 tons. The second simulation included seal predation in cod mortality which decreased the cod maximum sustainable yield by 98% at a fishing mortality of 0.02, which gave a fishing mortality of 0.19 and maximum sustainable yield of 275 000 tons for herring. This gives a 25 times increase of herring maximum sustainable yield compared to the result without predation on cod. The cod population dynamics is vulnerable to environmental changes and to secure a healthy and productive cod population the target fishing mortality should be kept in phase with current reproductive volume.