A　major　limiting　factor　for　DGGE-based　microbial　community　studies　is　that　the　fragments　should　not　be　much　longer　than　500 bp　for　successful　analysis.　However,　relatively　high-resolution　was　achieved　based　on　DGGE　of　the　long　18S　rDNA　fragment　(＞1500 bp),　which　might　be　surprising　due　to　the　known　decrease　in　DGGE　resolution　of　DNA　molecules　with　large　melted　regions.　A　unique　sequence　characteristic　was　found　in　a　specific　region　(ca.　275 bp,　named　the　NS1-end　region)　of　18S　rDNAs,　and　fungal　communities　separated　from　Hong　Qu　glutinous　rice　wine　brewing　system　was　used　to　reveal　the　relationship　between　high　resolution　capacity　and　the　unique　sequence　characteristics.　The　results　showed　that　DGGE　separation　of　the　long　18S　rDNA　fragments　depended　on　their　NS1-end　regions.　The　region　is　composed　of　a　sequence-variable　and　short-length　GC-poor　region　(ca.　160 bp)　and　a　GC-rich　region　(ca.　110 bp),　which　contribute　to　the　high　resolution　capacity　achieved　for　DGGE　of　the　long　18S　rDNA　fragments.　Thus　DGGE　of　the　long　18S　rDNA　fragment　is　recommended　as　a　target　fragment　for　studies　of　fungal　communities　whose　18S　rDNAs　possess　similar　sequence　characteristics.　Good　resolution　and　almost　full-length　18S　rDNA　sequences　can　thus　be　obtained　to　provide　more　accurate　and　reliable　analysis　of　fungal　communities.　Since　more　sequences　are　obtained　directly　from　the　PCR　product　through　the　long　rDNA　fragment　approach,　this　is　a　convenient　and　effective　approach　for　sequence-based　analysis　without　using　other　complementary　methods　such　as　an　rDNA　clone　library　method.　©　2016,　Springer　Science+Business　Media　Dordrecht.