Antibiotics　are　ubiquitous　pollutants　that　are　widely　found　in　aquatic　ecosystems,　where　the　bacterial　community　of　aquatic　plants　is　influenced　by　antibiotics.　However,　differences　between　endophyte　and　phyllosphere　bacteria　of　Lotus　from　above　and　below　surface　water　remains　unclear.　Lotus　samples　from　above　and　below　the　surface　water　were　collected　to　investigate　the　differences　in　endophyte　and　phyllosphere　bacteria　and　dominant　environmental　factors　in　regions　with　low　(L-)　and　high　(H-)　total　antibiotic　levels.　There　were　significant　differences　in　Shannon　diversity　between　endophyte　and　phyllosphere　bacteria　except　between　the　below-surface　water　phyllosphere　bacteria　and　below-surface　water　endophytes　in　both　L-antibiotic　and　H-antibiotic　regions,　with　higher　values　for　phyllosphere　bacteria.　The　dominant　phylum　in　all　phyllosphere　samples　was　Proteobacteria　(76.1%-92.5%),　while　Cyanobacteria　(47.8%-81.1%)　was　dominant　in　all　endophyte　samples.　The　dominant　source　of　above-surface　water　endophytes　was　below-surface　water　endophytes　(83.68-91.25%),　below-surface　water　phyllosphere　bacteria　(48.43-55.91%)　for　above-surface　water　phyllosphere　bacteria,　and　above-surface　water　endophytes　(53.83-61.80%)　for　below-surface　water　endophytes,　while　the　dominant　contributor　to　the　below-surface　water　phyllosphere　bacteria　was　also　below-surface　water　endophytes　(52.96-61.00%)　in　two　regions,　indicating　that　antibiotic　stress　changed　the　sink-source　relationship　between　endophytes　and　phyllosphere　bacteria.　The　physical-chemical　properties　of　surface　water　and　sediments　could　be　responsible　for　the　variations　in　the　above-　and　below-surface　water　endophytes　and　phyllosphere　bacteria　in　both　regions.　It　is　suggested　that　antibiotics　may　have　a　substantial　effect　on　endophyte　and　phyllosphere　bacterial　community.