By using the JavaFX standard doclet with the Javadoc tool, you can combine the documentation for your Java and JavaFX classes.
The Javadoc plugin is configured to only generate the XML output file, which is then used as an input to the Javafxdoc plugin.
<project> ... <reporting> <plugins> <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-javadoc-plugin</artifactId> <version>2.6.1</version> <configuration> <destDir>javadocs</destDir> <level>public</level> <sourcepath>${basedir}/src/main/java</sourcepath> <useStandardDocletOptions>false</useStandardDocletOptions> <doclet>com.sun.tools.xmldoclet.XMLDoclet</doclet> <additionalparam>-encoding ${project.build.sourceEncoding} -nohtml -o ${project.build.directory}/java_outfile.xml</additionalparam> <docletPath>${env.JAVAFX_HOME}\lib\shared\javafxdoc.jar</docletPath> </configuration> </plugin> <plugin> <groupId>net.sf.jfxdplugin</groupId> <artifactId>maven-javafxdoc-plugin</artifactId> <version>1.0</version> <configuration> <destDir>javafxdocs</destDir> <inputFiles> <inputFile>${project.build.directory}/java_outfile.xml</inputFile> </inputFiles> <show>public</show> <sourcePath>${basedir}/src/main/javafx</sourcePath> </configuration> </plugin> </plugins> ... </reporting> ... </project>