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I have a bunch of Tanganyikan cichlids I plan to move from my 55 gallon to a 90 gallon tank. Only problem is, my lamprologus multifaciatus had several sets of babies. About a dozen have grown large enough that I could probably catch them with an amount of effort.

For the small fry what would you suggest to do to catch them?

I have a feeling this is going to be a several day process.

well
Often they'll just jump into their shells as soon as you scare them
Then just pick up the shell and move it to another tank

or just get a small net for the straglers

you could also try a bottle trap for the stragglers.

http://www.cichlid-forum.com/articles/fish_trap.php