diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt
new file mode 100644
index 00000000000..9c35c64a1ea
--- /dev/null
+++ b/.ci/flake8_lint_include_list.txt
@@ -0,0 +1,2 @@
+lib/galaxy/jobs/runners/util/external.py
+lib/galaxy/util/bunch.py
diff --git a/.ci/flake8_wrapper_imports.sh b/.ci/flake8_wrapper_imports.sh
new file mode 100755
index 00000000000..22afed26991
--- /dev/null
+++ b/.ci/flake8_wrapper_imports.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+set -e
+
+flake8 `paste .ci/flake8_lint_include_list.txt`
diff --git a/.travis.yml b/.travis.yml
index 83463757ea4..2cae00653ec 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,6 +8,9 @@ env:
   - TOX_ENV=py27-unit
   - TOX_ENV=qunit
   - TOX_ENV=first_startup
+  - TOX_ENV=py27-lint-imports
+  - TOX_ENV=py27-lint-imports-include-list
+
 matrix:
   include:
   - os: osx
@@ -16,6 +19,8 @@ matrix:
   - os: osx
     env: TOX_ENV=py27-unit
     language: generic
+  allow_failures:
+  - env: TOX_ENV=py27-lint-imports
 
 before_install:
   - if [ `uname` == "Darwin"  ]; then bash -c "brew update && brew install python"; fi
diff --git a/setup.cfg b/setup.cfg
index 102507b9b14..4ae1306d579 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -7,3 +7,8 @@
 # 501 is line length
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 ignore = E128,E201,E202,E203,E501,E402,W503
+
+# For flake8-import-order
+# https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
+import-order-style = smarkets
+application-import-names = galaxy
diff --git a/tox.ini b/tox.ini
index 17abc6c9fb2..4045ed3646e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,8 +1,7 @@
 [tox]
-envlist = py27-lint, py27-unit, qunit, mako-count, web-controller-line-count, py33-lint, py34-lint, py35-lint
+envlist = py27-lint, py27-lint-imports, py27-lint-imports-include-list, py27-unit, qunit, mako-count, web-controller-line-count, py33-lint, py34-lint, py35-lint
 skipsdist = True
 
-
 [testenv:py27-lint]
 commands = bash .ci/flake8_wrapper.sh
 whitelist_externals = bash
@@ -31,6 +30,27 @@ deps =
     NoseHTML
     mock
 
+# Setup tox environments for linting all of Galaxy for imports and
+# just a subset we expect to pass (the include import list). Once the
+# include list is reduced to just the inverse of Galaxy's linting
+# blacklist these can both just be removed and flake8-import-order can
+# be added as a dependency to Galaxy's main linting task.
+[testenv:py27-lint-imports] 
+commands = bash .ci/flake8_wrapper.sh
+whitelist_externals = bash
+skip_install = True
+deps =
+    flake8<3
+    flake8-import-order
+
+[testenv:py27-lint-imports-include-list]
+commands = bash .ci/flake8_wrapper_imports.sh
+whitelist_externals = bash
+skip_install = True
+deps =
+    flake8<3
+    flake8-import-order
+
 [testenv:qunit]
 commands = bash run_tests.sh -q
 whitelist_externals = bash