How do I link between markdown documents in doxygen?

As per Doxygen 1.8.7 there are three ways to do this:

• Use a standard markdown hyperlink as described in your original question.
• Use a @ref and prefix the target with md_ along with any subdirectories.
• Name the page and use @ref to refer to the name.

The first method is straightforward and this will also work without Doxygen (e.g. when browsing your code repository on Github).

[Go to this page](subdir/MyOtherPage.md)

Whereas the second method you’ll need to link it like this:

[Go to this page](@ref md_subdir_MyOtherPage)

Apparently this also is the way prescribed by the Doxygen’s primary author.

Lastly in the third method you’ll need to have a name for the target page and then link to that name. Example:

In MyOtherPage.md have this as the header

# My Other Page Title {#MyOtherPageName}

then link it like so

[Go to this page](@ref MyOtherPageName)