The main benefit is that markdown is really readable _without_ rendering. You don't need to edit and then open in a browser.
You can comfortably read plaintext that has a little structure, while HTML adds some ceremony that makes it a bit harder to glance at the material as the tags are much more in your face.
# title
this is the paragraph
is more natural to write than:
<html> <head>...<head/> <body> <h1> title </h1> <p>this is the paragraph</p> </body> </html>
when you're just jotting some thoughts down.