It still may or may not work. Your best bet is to match voltage, latency and speeds but even 2 different kits from the same brand can have different sub timings. There are only a few companies that make DRAM like Samsung, Elpida, Hynix, Micron etc. So you could buy 2 different 1.5v DDR3 1600 kits from GSkill and get RAM modules in one made by Elpida and modules in the other from Powerchip. While it would probably work together the sub timings that aren't user adjustable may very well be slightly different.
Matching speed, voltage and latency will most likely work although I would still use memtest to make sure it isn't throwing errors.