These are both joins. they are just two different syntactical representations for joins. The first one, (using the "Join" keyword, is the current ANSI Standard (as of 1992 I think).
In the case of inner joins only, the two differeent representations are functionally identical, but the latter ANSI SQL92 standard syntax is much moire readable, once you get used to it, because each individual join condition is associated with the pair of intermediate resultsets being joined together, In the older representation, the join conditions are all together, along with the overall queries' filter conditions, in the where clause, and it is not as clear which is which. This makes identifying bad join conditions (where for example, an unintended cartesian product will be generated) much more difficult.
But more important, perhaps, is that, when performing an outer Join, in certain scenarios, the older syntax is NOT equivilent, and in fact will generate the WRONG resultset.
You should transition to the newer syntax for all your queries.