It doesn't mean exactly what it seems to -- nothing can see in total darkness because the eye needs some light to work. However, you say that some animals can "see in the dark" when they can see in very little light.
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"Seeing in the dark" typically refers to having the ability to see clearly in low-light or dark conditions. This can be a natural ability possessed by some animals or a capability enhanced by technology such as night vision goggles for humans.