diff --git a/docs/api-longbow.apps.rst b/docs/api-longbow.apps.rst
new file mode 100644
index 0000000..8ef6f05
--- /dev/null
+++ b/docs/api-longbow.apps.rst
@@ -0,0 +1,67 @@
+Application Plugins
+===================
+
+Module contents
+---------------
+
+.. automodule:: longbow.apps
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.amber module
+-------------------------
+
+.. automodule:: longbow.apps.amber
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.charmm module
+--------------------------
+
+.. automodule:: longbow.apps.charmm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.chemshell module
+-----------------------------
+
+.. automodule:: longbow.apps.chemshell
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.desmond module
+---------------------------
+
+.. automodule:: longbow.apps.desmond
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.gromacs module
+---------------------------
+
+.. automodule:: longbow.apps.gromacs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.lammps module
+--------------------------
+
+.. automodule:: longbow.apps.lammps
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.apps.namd module
+------------------------
+
+.. automodule:: longbow.apps.namd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
diff --git a/docs/api-longbow.rst b/docs/api-longbow.rst
new file mode 100644
index 0000000..411da27
--- /dev/null
+++ b/docs/api-longbow.rst
@@ -0,0 +1,67 @@
+Core API
+========
+
+Module contents
+---------------
+
+.. automodule:: longbow
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.applications module
+---------------------------
+
+.. automodule:: longbow.applications
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.configuration module
+----------------------------
+
+.. automodule:: longbow.configuration
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.entrypoints module
+--------------------------
+
+.. automodule:: longbow.entrypoints
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.exceptions module
+-------------------------
+
+.. automodule:: longbow.exceptions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.scheduling module
+-------------------------
+
+.. automodule:: longbow.scheduling
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.shellwrappers module
+----------------------------
+
+.. automodule:: longbow.shellwrappers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.staging module
+----------------------
+
+.. automodule:: longbow.staging
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
diff --git a/docs/api-longbow.schedulers.rst b/docs/api-longbow.schedulers.rst
new file mode 100644
index 0000000..d525471
--- /dev/null
+++ b/docs/api-longbow.schedulers.rst
@@ -0,0 +1,51 @@
+Scheduler Plugins
+=================
+
+Module contents
+---------------
+
+.. automodule:: longbow.schedulers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.schedulers.lsf module
+-----------------------------
+
+.. automodule:: longbow.schedulers.lsf
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.schedulers.pbs module
+-----------------------------
+
+.. automodule:: longbow.schedulers.pbs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.schedulers.sge module
+-----------------------------
+
+.. automodule:: longbow.schedulers.sge
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.schedulers.slurm module
+-------------------------------
+
+.. automodule:: longbow.schedulers.slurm
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+longbow.schedulers.soge module
+------------------------------
+
+.. automodule:: longbow.schedulers.soge
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
diff --git a/docs/index.rst b/docs/index.rst
index e2d7685..1779ece 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -43,6 +43,10 @@ Support for any issues arising from using Longbow, whether these are questions,
    :maxdepth: 2
    :caption: API Documentation:
 
+   api-longbow
+   api-longbow.apps
+   api-longbow.schedulers
+
 .. toctree::
    :maxdepth: 2
    :caption: Developers Documentation: