Effects　of　the　technologies　of　clone　library　and　high　throughout　sequencing　for　revealing　microbial　community　structure　and　functional　bacteria　in　a　biofilter　which　simultaneously　removes　iron,　manganese　and　ammonia　were　compared.　15057　sequences　with　32　classifications　in　class　level　were　obtained　after　the　high　throughout　sequencing　process,　while　there　are　9classified　groups　in　clone　library.　The　former　revealed　more　diversity　of　bacterial　community　structure.　However,　in　the　functional　bacteria　analysis　process,　some　nitrifiers　or　iron　and　manganese　bacteria　which　were　detectable　in　one　sequencing　analysis　process　were　not　appeared　in　the　other　process.　Comparing　with　using　these　two　technologies　individually　in　the　analysing　process,　the　combined　using　can　compensate　for　each　other　and　reveal　the　functional　bacteria　better.　©　2016,　Editorial　Board　of　China　Environmental　Science.　All　right　reserved.