diff --git a/doc/org-manual.org b/doc/org-manual.org
index a38dbec4a..b62c52e61 100644
--- a/doc/org-manual.org
+++ b/doc/org-manual.org
@@ -10814,9 +10814,11 @@ and verbatim string is not processed for Org specific syntax; it is
 exported verbatim.
 
 #+vindex: org-fontify-emphasized-text
+#+vindex: org-emphasis-alist
 To turn off fontification for marked up text, you can set
-~org-fontify-emphasized-text~ to ~nil~.  To narrow down the list of
-available markup syntax, you can customize ~org-emphasis-alist~.
+~org-fontify-emphasized-text~ to ~nil~.  For more fine-tuned
+fontification consider themes. It is possible to customize
+~org-emphasis-alist~ variable, but it will be deprecated.
 
 ** Subscripts and Superscripts
 :PROPERTIES:
diff --git a/lisp/org.el b/lisp/org.el
index cb1b58c51..ea62ae0b2 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -3771,6 +3771,25 @@ newline      The maximum number of newlines allowed in an emphasis exp.
 
 You need to reload Org or to restart Emacs after setting this.")
 
+(defun org-set-emphasis-alist (var value)
+  "Set VAR (`org-emphasis-alist') to VALUE and check it for ignored characters.
+Warn user that Org syntax can not be extended with new emphasis markers
+if such attempt is detected.  The function is intended for :set argument
+of `defcustom'."
+  (set var value)
+  (let ((unsupported
+	 (delq nil
+	       (mapcar
+                (lambda (entry)
+                  (let ((marker (car entry)))
+                    (unless (member marker '("*" "/" "_" "=" "~" "+")) marker)))
+                value))))
+    (when unsupported
+      (message "Warning! Unsupported markup characters '%s' detected in `%s'"
+	       (mapconcat #'identity unsupported " ")
+	       (symbol-name var))))
+  value)
+
 (defcustom org-emphasis-alist
   '(("*" bold)
     ("/" italic)
@@ -3779,23 +3798,41 @@ You need to reload Org or to restart Emacs after setting this.")
     ("~" org-code verbatim)
     ("+" (:strike-through t)))
   "Alist of characters and faces to emphasize text.
+Warning! This variable will be deprecated in favor of themes.
+
 Text starting and ending with a special character will be emphasized,
 for example *bold*, _underlined_ and /italic/.  This variable sets the
 marker characters and the face to be used by font-lock for highlighting
 in Org buffers.
 
+Do not change the characters and do not add new ones to use custom
+markers for existing styles or to introduce new styles.  Org syntax is
+not meant to be configurable and such modifications will not work with
+export.
+
 You need to reload Org or to restart Emacs after customizing this."
   :group 'org-appearance
   :set 'org-set-emph-re
   :version "24.4"
   :package-version '(Org . "8.0")
+  :set #'org-set-emphasis-alist
   :type '(repeat
-	  (list
-	   (string :tag "Marker character")
-	   (choice
-	    (face :tag "Font-lock-face")
-	    (plist :tag "Face property list"))
-	   (option (const verbatim)))))
+          (group
+           (choice
+            :tag "Marker"
+            (const :tag "*Bold*" "*")
+            (const :tag "/Italic/" "/")
+            (const :tag "_Underline_" "_")
+            (const :tag "+Strike-through+" "+")
+            (const :tag "=Verbatim=" "=")
+            (const :tag "~Code~" "~")
+            ;; To warn users that it does not work.
+            (string :tag "Unsupported ignored character"))
+           (choice
+            :tag "Font"
+            (face :tag "Face")
+            (plist :tag "Property list"))
+           (option (const verbatim)))))
 
 (defvar org-protecting-blocks '("src" "example" "export")
   "Blocks that contain text that is quoted, i.e. not processed as Org syntax.