The difference is whether you will be targeting the .Net Core Framework or the Full .Net Framework. And this difference shows up for example in the project.json file.
Another thing to know about is that when you use the "ASP.NET Core Web Application (.NET Framework)" template it's much easier to link to .Net Library Projects that target the full framework when using Visual Studio. It's possible to do it using the "ASP.NET Core Web Application (.NET Core)" template but it requires some manual editing of the project.json file.
It may also be worth mentioning that if you target the Full Framework the web application must be deployed on Windows, whereas targeting the .Net Core framework allows the web application to be deployed to non-Windows environments. But the .Net Core Framework is not as feature rich as the Full Framework. (It has no drawing routines for resizing images for instance). You can read more about choosing the right framework here: https://docs.asp.net/en/1.0.0-rc1/getting-started/choosing-the-right-dotnet.html
Either way, no matter which of these two templates you select, you will be creating a project for creating an ASP.NET Core application.
Here is what the solution looks like in Visual Studio 2015 Update 3 when "ASP.NET Core Web Application (.NET Core)" is chosen (with Empty option):
And here is its project.json file:
Here is what the solution looks like in Visual Studio 2015 Update 3 when "ASP.NET Core Web Application (.NET Framework)" is chosen (with Empty option):
And here is its project.json file:
ASP.NET Core can run on top of .NET Core or the full .NET Framework . So there's a template depending on whether you want to build on .NET Core or the full .NET Framework.
Here's an infographic that Microsoft put together that visually demonstrates the concept:
No matter which template you choose, you can always edit your configuration to target both at the same time. But the templates just help you get started with one or the other.
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