From the man page for latexmk (http://manpages.ubuntu.com/manpages/raring/man1/latexmk.1L.html):
[...] the -recorder option with latex and pdflatex. In (most) modern versions of these programs, this results in a file of extension .fls containing a list of the files that these programs have read and written.
Latexmk specifies this option in its latex commands and so produces temporary files with this extension in latex projects.