The destination anchor for a link in an HTML page may be any element with an id
attribute. See Links on the W3C site. Here's a quote from the relevant section:
Destination anchors in HTML documents
may be specified either by the A
element (naming it with the name
attribute), or by any other element
(naming with the id attribute).
Markdown treats HTML as HTML (see Inline HTML), so you can create your fragment identifiers from any element you like. If, for example, you want to link to a paragraph, just wrap the paragraph in a paragraph tag, and include an id:
<p id="mylink">Lorem ipsum dolor sit amet...</p>
Then use your standard Markdown [My link](#mylink)
to create a link to fragment anchor. This will help to keep your HTML clean, as there's no need for extra markup.