Hopefully you have a digital voltmeter that you can trust. If not, get one.
Curious what your ammeter is supposed to read. Just alternator output, or does it measure all current in/out of your batteries. If the meter came with the boat, it's likely just alternator output. New (smarter) systems put a shunt in the negative leg to the house bank and measure current both ways. There are shunt meters that only do alternator output.
First step should be to measure the output voltage of the alternator, engine running. If it's more than battery voltage you should see charge current, hence a meter/wiring problem. If there's no/low alternator voltage you have an issue with the alternator or its regulator - don't confuse the two. Problems with either will prevent output from the alternator.
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