First, make sure both focus settings are set on spot. There is one AF setting and a second focus setting on a different menu. Should be set to AF, Full-time AF off, Spot Focus.
Next, the camera sucks at focus in low light. A spotting light of some sort really helps. I just use a 4aa pocket light hooked to my strobe arm, otherwise the camera will hunt endlessly for focus and then pick up the strongest signal.
For smaller, hard to focus objects, you can focus on something strong at the same distance, hold the button halfway, move to your subject and shoot.
Another thing that could be happening is that the issue isn't camera focus, but a slight blur from a moving subject. Since you're using a strobe, try upping your shutter speed to the next level. If you're shooting at 1/60, try 1/80. You might have to open your lens a bit more to make up for it. I've found the camera to be very happy at f5.6@1/60 in the dark waters of Monterey. You can go easily to 1/80 or 1/100 in clearer tropical water without dropping your f-stop. If you are using a very low f-stop, as f2.8 or f3.5, you'll have poor depth of focus and blur either the foreground or background. If possible, stay with at least f4.5 which works fine for wide angle shots even in darker water.