If your transom looks like the one in this ad
http://sailingtexas.com/201009/soday17139.html then it looks like the deck forms a lip over it for about an inch-wide strip of overlap. First I would check whether the overlap actually is as big as it could be. Possibilities include the transom not extending all the way to the deck, so the overlap falls short.
If there's sufficient overlap you should be able to glue these parts back together. I think you should be able to even use epoxy glue - after running some sandpaper in the gap and cleaning it to get out any grease. A high quality epoxy glue (not the $5 dual syringes from the H/W store) would work - you need something that's not runny. There's an all-purpose epoxy paste that's sold under the MarineTex brand - it's not primarily a glue, but given the large area should work pretty well - the biggest challenge would be to get it applied to the inside of the crack.
Epoxy glue in the caulk-gun cartridge from SystemThree or WestSystem if you can get it would work.
Or you could use an adhesive sealant like 3m 5200 (or perhaps a slightly less aggressively bonding formulation not sure about product number, but in the 4000's) or competitors' similar products. (Don't use a silicone sealant, like bathroom caulk).
If there's any hidden defect, like the transom is too short to overlap properly, then you might need to glass over the joint to get it to hold. Aesthetically the choice would be to work from the inside, but drilling the access ports is probably not practical. Let's hope that you do have sufficient overlap, but you can always put a strip of fiberglass over the outside of the joint. That would make a strong and secure connection, but would be a visible repair.