It honestly doesn't really matter. Both ingest Markdown, apply a theme, and spit out HTML which you then copy to your HTTP server. It's sort of like asking "w

It honestly doesn't really matter. Both ingest Markdown, apply a theme, and spit out HTML which you then copy to your HTTP server. It's sort of like asking "which version control do you prefer? Mercurial or Git" or "which build tool do you prefer? clang or gcc." Your choice in the matter doesn't really impact the end result, just your own workflow. Jekyll is probably more popular simply because GitHub has it integrated with GitHub Pages.