I have a 24V trolling motor. One of my flooded cell batteries failed this week. The other battery tests very strong. My on board charger can charge both flooded cell and AMG batteries. Can I buy an AMG battery and pair it with the flooded cell battery?

You'll get mixed opinions but yes you can mix batteries. Problem is the lower amp rated one will draw down the other and in time will shorten its life. Hate to say it but for longevity its best to replace both with a matching set.

I was always told if your running a 24v system, replace both at the same time with the same type battery. That’s what I have always done. Back years ago I would run Walmart brand and it never failed that one would die just after the warranty would go out. I switched to Interstate and had good luck till my last set. I switched to Duracell AGM now. Time will tell. But so far so good.
I’m sure there are some battery experts on here though that will chime in for your issue. Good luck.

Your system will only be as good as your weakest battery. All it will cost to give it a try is the possibility of a short trip if your trolling motor goes down. I have replaced only one if the set was less than 2 years old, otherwise I replaced all of them.

Try an AGM

I bought a pair of Duracell AGM's at Sams for $158/ea.
Thanks for your help.

That’s a good option.