In standard Markdown, place an anchor <a name="abcd"></a> where you want to link to and refer to it on the same page by [link text](#abcd).
(This uses name= and not id=, for reasons explained in this answer.)
Remote references can use [link text](http://...#abcd) of course.
This works like a dream, provided you have control over the source and target texts. The anchor can even appear in a heading, thus:
### <a name="head1234"></a>A Heading in this SO entry!
produces:
A Heading in this SO entry!
and we can even link to it so:
and we can even https://stackoverflow.com/questions/6695439/how-to-link-to-a-named-anchor-in-multimarkdown(#head1234) to it so:
(On SO, the link doesn’t work because the anchor is stripped.)