Rmarkdown includes a number of themes as described on the rmarkdown site.

To add a theme specify the following at the beginning or towards the end of the _site.yml. It makes sense to include it near the top as it saves on scrolling when you want to change it (and you will).

output:
  html_document:
    theme: flatly
    highlight: textmate

At the time of writing the available themes that you might want to try are cerulean, cosmo, flatly, journal, lumen, paper, readable, sandstone, simplex, , spacelab, united, yeti (the following were not available cyborg, darkly, slate, superhero). See the rmarkdown site and the Bootswatch site for the theme origins with the wildly popular bootstrap. If none of that makes much sense, it will do when you read up on the links.