\documentclass{article}
\usepackage{libertine,media9,polyglossia}
\setdefaultlanguage[variant=british]{english}
\setotherlanguage[]{hebrew}

\begin{document}
\marginpar{\includemedia[
  label=song49,
  activate=pagevisible,
  deactivate=pageinvisible,
  noplaybutton,
  flashvars={source=http://www.kfeuerherm.ca/IntHeb/BBE.mp3&hidebar=true},
  transparent
]{\makebox[1cm]{x}}{APlayer.swf}\mediabutton[mediacommand=song49:playPause,tooltip={Play/Pause}]{(P)}\mediabutton[mediacommand=song49:play[(0.0)],tooltip={Reset}]{(R)}} 
%\begin{RTL}
\mediabutton[
  mediacommand=song49:play[(0.65)],
  mediacommand=song49:pause[(1.45)],
  overface=ONE
]{בראשׁית}
\mediabutton[
  mediacommand=song49:play[(1.8)],
  mediacommand=song49:pause[(2.45)],
  overface=TWO
]{ברא}
\mediabutton[
  mediacommand=song49:play[(2.8)],
  mediacommand=song49:pause[(3.8)],
  overface=THREE
]{אלהים}
%\end{RTL}
\end{document}
