Cause of Wallace line First off, I am a biologist, not an earth scientist. 

Very recently I heard about a very interesting biological phenomenon that has its origins rooted in geology : The Wallace Line. 

From a biological perspective, this is very interesting. Wikipedia explains it very, but in short: The Wallace Line describes that in south east Asia there is a very strong divide in occurrence of species when comparing everything from Bali westward, and everything from Lombok eastward. e.g. large mammals characterizing Sumatra and Java are: Tigers, Elephants and Rhinos. Whereas eastward of the Wallace Line, you have your Marsupials. The same goes for many other different animal and plant species. 

Explanation given is that many many many years ago when the sea level was much lower, there was an oceanic divide between east and west of south east Asia. This is supposed to be the result of tectonic movement. However, I have not been able to find a detailed explanation what could have caused this deeper oceanic divide. If I look at maps of tectonic plates and tectonic activity in the region, there are no tectonic boundaries that overlap the Wallace line. 

So all this leading to my question: What could have been the cause of the this deep divide? 

Here a link of the Wallace Line

Here a link of Indonesian Bathymetry
So all this leading to my question: What could have been the cause of
  the this deep divide?


Think about what animals need to travel between Islands.  It's very difficult unless the water between the islands either drops or freezes over (Deer, for example, have crossed from New Jersey to Staten Island when the Hudson River freezes over), but the ocean doesn't freeze near the Wallace line.

Or, during ice ages when sea level falls as much as 410 feet, Islands can be joined as sea level drops.   Japan, for example, a land-bridge formed through Hokaido to mainland Asia.  Likewise, the UK connects to France and the Bering Straight becomes land as well.

There's nothing particularly remarkable about the water over the Wallace line other than it being too deep for any land bridges to form during ice ages.  The relevant geological feature for land bridges is shallow oceans/seas/bays/straights/channels, etc.   The Java sea is sufficiently shallow that all the islands Northwest of the Wallace line are joined when sea level falls.    

It was pointed out that it's rough water too, but that's not the primary reason.   The primary reason is simply the ocean's depth and width.  Animals have little incentive to try to cross any fairly large body of ocean.  Animals sometimes migrate across raging rivers, but in that situation the other side is clearly visible.  The islands on each side of the Wallace line, even with the sea level drop, would (I assume), appear very far away to the eye, if they could be seen at all.