Question: Some islands are called isle like "Isle of Man", "Isle of Tortuga" and the "British Isles". Other islands are called island, like "Island of Malta" or "Island of Cyprus".

What is the difference between the words?
How to know if a land mass confined by water is called an isle or an island?

Answer: 
In practice there is no difference, they can be used interchangeably, but *isle* is archaic. Anything called *isle* can also be referred to as an island.

I had thought that *isle* was just an archaic version of *island*, but it turns out the words are actually not related:

> 
> [island](http://www.etymonline.com/index.php?term=island&allowed_in_frame=0) (n.)
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> 
> 1590s, earlier yland (c.1300), from Old English igland "island," from ieg "island" (from Proto-Germanic \*aujo "thing on the water," from PIE \*akwa- "water;" see aqua-) + land "land." Spelling modified 15c. **by association with similar but unrelated isle**. An Old English cognate was ealand "river-land, watered place, meadow by a river." In place names, Old English ieg is often used of "slightly raised dry ground offering settlement sites in areas surrounded by marsh or subject to flooding" [Cambridge Dictionary of English Place-Names]. Related: Islander.
> 
> 
> [isle](http://www.etymonline.com/index.php?term=isle) (n.)
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> 
> late 13c., from Old French ile, earlier isle, from Latin insula "island," of uncertain origin, perhaps (as the Ancients guessed) from in salo "(that which is) in the sea," from ablative of salum "the open sea." The -s- was restored first in French, then in English in the late 1500s.
> 
> 
>
There is no difference in the words' meanings, they both denote a landmass surrounded by water.
The [definition](http://www.thefreedictionary.com/isle) from one of the dictionaries sums it up nicely about "isle", I think:

> 
> Poetic except when cap. and part of place name; an island, esp a small one
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> 
> 

So "isle" has the same meaning, just more poetic (it is a monosyllabic word), more often used with small islands. As for geographic names - they were named like that at some time, so someone chose "isle" over "island" while naming them.