Use the Basins tool

http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#//009z0000004z000000.htm

Try to use SAGA software also.

Try the Soil and Water Assessment Tool (SWAT). 

No matter what tool you use, you will still have to do almost the same. If you need to nail 1000 nails, you can use a hammer or a nailing pistol, but the nails still need to be pushed in. So, here is a quick, short suggestion that may help you get started.

1. Extract the end points of your streams.

2. Extract elevation for both ends (using your DTM).

3. Select the ends with the lowest elevation and this will be your pour points.

4. Run the watershed tool, or basin or whatever other tool you have in mind for all points.

You may not be familiar with loops, but in Model Builder they allow you to run the same analysis on all the features of a given layer (also called class). It will take some time to do its business but it is all computing time, you can go have lunch or take a nap on the meantime.

Hope it helps

Rafael

Thanks every one..I shall try the options.