How to change the highlighting color in JavaFX?

Also you can use -fx-highlight-fill on text-area class selector.

.text-area {
    -fx-highlight-fill: green;
}

I think Uluk Biy has answered it great way.

But the reality is styling using CSS does not override the -fx-focus-color: #0093ff, rather it will overlap. If you use -fx-focus-color: red , it will get mixed with default blue color and show a shade of grey like color. The css attribute -fx-accent has no issues.

Look at caspian.css (JavaFX 2) or modena.css (JavaFX 8)

.root {
    /* A bright blue for highlighting/accenting objects.  For example: selected
     * text; selected items in menus, lists, trees, and tables; progress bars;
     * default buttons.
     */
    -fx-accent: #0093ff;

    /* A bright blue for the focus indicator of objects. Typically used as the
     * first color in -fx-background-color for the "focused" pseudo-class. Also
     * typically used with insets of -1.4 to provide a glowing effect.
     *
     * TODO: should this be derived from -fx-accent?
     */
    -fx-focus-color: #0093ff;
}

Change these colors according to their usages.