HTML5 enabled browsers to have a video element that you can use to play a video on your site. To let you know, flowplayer and other flash based video streaming players use the FLV format.
It has the same encoding as H.264. FFMPEG can convert videos to FLV, feel free to work it with flowplayer.
Use the flvtool2 for reading and writing FLV metadata from and to the file.
Use the tools to create your videos and stream them through flowplayer.