The mkdocs_tree extension will allow you to load a hierarchy of markdown files into your mkdocs project.

Installation

You can install the mkdocs_tree package using pip or easy_install

$ pip install mkdocs_tree
$ easy_install mkdocs_tree

Usage

Create a folder structure of *.md files somewhere in your documents root, for instance

[-] ./docs/api/mkdocs
 |- index.md
 |- [+] contrib
 |- [-] utils
 |   |- index.md

To serve this hierarchy, you will need to include the mkdocs_tree extension in your mkdocs.yml configuration file:

mkdocs_extensions:
    - mkdocs_tree

Once that is included, you can load your folder hierarchy by including it in your pages configuration:

pages:
    - ['tree:api/mkdocs', 'API', 'mkdocs']

As you can see, the syntax is tree:<path/to/root>. It will load only a single page to the API header, named mkdocs, but register all the sub-pages for reference within the documentation.