Tagging fish has helped with scientific research. Migration patterns have been identified with this method. A small metal dowel is inserted in the fish's snout. As not to mix with the wild salmon. Then when the salmon come back the to spawn they will come back to the stream and that stream slowly restocks its self.
Many people think that hatchery fish lack certain natural instincts that the wild salmon have.
Many hatchery fish do make the entire journey and they pass their genes on to their offspring. Hatchery fish are more likely to get diseases easier than wild fish in some people's opinion. There has been no strong evidence to prove this theory. But that because the hatchery fish live in closer living quarters disease spreads faster. However in the wild hatchery fish seem no more susceptible to disease than the wild fish.