| Sacciolepis indica (L.) Chase | MAKS2474, MAKS2478 |
| Sagittaria aginashi Makino | MAKS2112 |
| Sagittaria pygmaea Miq. | MAKS2110 |
| Sagittaria trifolia L. | MAKS0809, MAKS2113 |
| Sagittaria trifolia L. var. edulis (Siebold) Ohwi | MAKS2114, MAKS2115 |
| Salix sachalinensis Fr. Schmidt | MAKS1732 |
| Salomonia oblongifolia DC. | MAKS0193, MAKS0194 |
| Salvia glabrescens Makino | MAKS1377, MAKS1378, MAKS1379 |
| Salvia japonica Thunb. | MAKS0479 |
| Salvia nipponica Miq. | MAKS2240 |
| Salvia plebeia R. Br. | MAKS1375, MAKS1376 |
| Sambucus racemosa L. subsp. sieboldiana (Miq.) Hara | MAKS2026 |
| Sanicula chinensis Bunge | MAKS2047 |
| Sapindus mukorossi Gaertn. | MAKS1191 |
| Sapium japonicum (Siebold et Zucc.) Pax et Hoffm. | MAKS0084, MAKS0616, MAKS1592, MAKS1593, MAKS1594 |
| Sapium sebiferum (L.) Roxb. | MAKS0083, MAKS0085, MAKS0086, MAKS0087 |
| Saponaria | MAKS0196 |
| Sarcandra glabra (Thunb.) Nakai | MAKS1623 |
| Saururus chinensis (Lour.) Baill. | MAKS1622, MAKS0717 |
| Saussurea gracilis Maxim. | MAKS1037 |
| Saussurea japonica (Thunb.) DC. ? | MAKS1344 |
| Saussurea nipponica Miq. | MAKS1296 |
| Saussurea nipponica Miq. subsp. savatieri Kitam. | MAKS1005 |
| Saussurea pulchella Fischer | MAKS0449 |
| Saussurea sp. | MAKS1298 |
| Saussurea triptera Maxim. | MAKS1036 |
| Saxifraga fortunei Hook. fil. var. | MAKS1982 |
| Saxifraga fortunei Hook. fil. var. crassifolia (Engl. et Irmsch.) Nakai | MAKS1984 |
| Saxifraga fortunei Hook. fil. var. incisolobata (Engl. et Irmsch.) Nakai | MAKS1983 |
| Saxifraga fusca Maxim. var. kikubuki Ohwi | MAKS1980 |
| Saxifraga merkii Fisch. var. idsuroei (Franch. et Savat.) Engl. ex Matsum. | MAKS1981 |
| Scabiosa japonica Miq. | MAKS1292 |
| Schisandra chinensis (Turcz.) Baill. | MAKS0081, MAKS0221 |
| Schisandra nigra Maxim. | MAKS0213 |
| Schizocodon soldanelloides Siebold et Zucc. | MAKS1077, MAKS1078 |
| Schizopepon bryoniaefolius Maxim. | MAKS2065 |
| Schizophragma hydrangeoides Siebold et Zucc. | MAKS1963 |
| Sciadopitys verticillata (Thunb.) Siebold et Zucc. | MAKS1742, MAKS1743 |
| Scilla scilloides (Lindl.) Druce | MAKS0524, MAKS0800 |
| Scirpus tabernaemontani Gmel. | MAKS2568, MAKS2564 |
| Scirpus triqueter L. | MAKS2565 |
| Scurrula yadoriki (Siebold) Danser | MAKS0680 |
| Scutellaria baicalensis Georgi | MAKS1382, MAKS1383 |
| Scutellaria dependens Maxim. | MAKS0272 |
| Scutellaria indica L. | MAKS2241, MAKS2242 |
| Scutellaria sp. | MAKS0268, MAKS0235 |
| Scutellaria stigillosa Hemsl. | MAKS1381, MAKS2286 |
| Securinega suffruticosa (Pallas) Rehder var. japonica (Miq.) Hurusawa | MAKS1544, MAKS1545, MAKS1596 |
| Sedirea japonica Garay et Sweet | MAKS0752 |
| Sedum aizoon L. var. floribundum Nakai | MAKS2105 |
| Sedum bulbiferum Makino | MAKS2100 |
| Sedum lineare Thunb. | MAKS0833, MAKS2101 |
| Sedum makinoi Maxim. | MAKS0831 |
| Sedum uniflorum Hook. et Arnott subsp. japonicum (Siebold et Miq.) H. Ohba | MAKS0832, MAKS2098 |
| Semiaquilegia adoxoides (DC.) Makino | MAKS0053 |
| Senecio cannabifolius Less. | MAKS1034, MAKS1303 |
| Senecio flammeus Turcz. ex DC. subsp. glabrifolius (Cufod.) Kitam. | MAKS1327 |
| Senecio nemorensis L. | MAKS1033, MAKS1315 |
| Senecio nemorensis L. ? | MAKS1035 |
| Senecio nikoensis Miq. | MAKS1029, MAKS1032, MAKS1329 |
| Serratula coronata L. subsp. insularis (Iljin) Kitam. | MAKS1038 |
| Serratula coronata L. subsp. insularis (Iljin) Kitam. ? | MAKS1039 |
| Setaria chondrachne (Steud.) Honda | MAKS2421 |
| Setaria faberi Herrm. | MAKS2479 |
| Setaria italica Beauv. | MAKS2463, MAKS2495 |
| Setaria pallide-fusca (Schumach.) Stapf et C. E. Hubb. | MAKS2472, MAKS2490, MAKS2466 |
| Setaria sp. | MAKS2493 |
| Setaria viridis (L.) Beauv. | MAKS2473 |
| Setaria viridis (L. ) Beauv. | MAKS2494 |
| Setaria x pycnocoma (Steud.) Henrald ex Nakai | MAKS2491 |
| Siegesbeckia orientalis L. subsp. pubescens (Makino) Kitam. | MAKS0584, MAKS0943, MAKS1040, MAKS1041 |
| Silene firma Siebold et Zucc. | MAKS0200 |
| Sium ninsi L. | MAKS2051 |
| Sium suave Walter subsp. nipponicum (Maxim.) Sugimoto | MAKS2053 |
| Skimmia japonica Thunb. | MAKS1223 |
| Smilacina japonica A. Gray | MAKS0781, MAKS2364, MAKS2365, MAKS2367 |
| Smilax biflora Siebold et Zucc. | MAKS0345 |
| Smilax biflora Siebold ex Miq. | MAKS2374 |
| Smilax biflora Siebold ex Miq. var. trinervula (Miq.) Hatus. | MAKS2371 |
| Smilax china L. | MAKS0518, MAKS2381, MAKS2383 |
| Smilax nipponica Miq. | MAKS0787, MAKS2382 |
| Smilax nipponicun Miq. ? | MAKS2375 |
| Smilax riparia A. DC. var. ussuriensis (Regel) Hara et T. Koyama
Smilax nipponica Miq. | MAKS2378 |
| Smilax sebeana Miq. | MAKS2379 |
| Smilax sieboldii Miq. | MAKS0786, MAKS2376 |
| Smilax sp. | MAKS2377, MAKS2384 |
| Solidago virgaurea L. subsp. asiatica Kitam. | MAKS1042, MAKS1043, MAKS1314 |
| Sonchus brachyotus DC. | MAKS0578 |
| Sonchus oleraceus L. | MAKS0606, MAKS1323 |
| Sorbaria sorbifolia (L.) A. Br. ? | MAKS1927 |
| Sorbus alnifolia (Siebold et Zucc.) C. Koch | MAKS1686, MAKS1887 |
| Sorbus commixta Hedl. | MAKS1889 |
| Sorbus matsumurana (Makino) Koehne | MAKS1890 |
| Sorghum sp., Hordeum vulgare L. | MAKS2451 |
| Spinacia oleracea L. | MAKS1416 |
| Spiraea chamaedryfolia L. var. pilosa (Nakai) Hara | MAKS2667 |
| Spiraea dasyantha Bunge | MAKS1926 |
| Spiraea japonica L. fil. | MAKS1925, MAKS2666 |
| Spiraea nipponica Maxim. var. tosaensis (Yatabe) Makino | MAKS1931 |
| Spiraea prunifolia Siebold et Zucc. | MAKS1930 |
| Spiraea salicifolia L. | MAKS1928 |
| Spiraea thunbergii Siebold ex Blume | MAKS1932 |
| Spiranthes sinensis (Pres.) Ames var. amoena (M. Bieberson) Hara | MAKS0753, MAKS2205 |
| Spodiopogon sibiricus Trin. | MAKS2438, MAKS2416, MAKS2424 |
| Sporobolus fertilis (Steud.) W. Clayton | MAKS2400, MAKS2520 |
| Spuriopimpinella calycina (Maxim.) Kitag. | MAKS2052 |
| Stachys riederi Chamisso var. intermedia (Kudo) Kitam. | MAKS1387 |
| Stachys sieboldii Miq. | MAKS0480, MAKS1386 |
| Stachyurus praecox Siebold et Zucc. | MAKS0197 |
| Staphylea bumalda (Thunb.) DC. | MAKS1175 |
| Stellaria monosperma Buch.-Hamilt. var. japonica Maxim. | MAKS0201 |
| Stemona ? | MAKS2139 |
| Stemona japonica Miq. | MAKS2136, MAKS2137, MAKS2138 |
| Stephanandra incisa (Thunb.) Zabel | MAKS1923 |
| Stephania japonica (Thunb.) Miers | MAKS0125 |
| Stephanotis lutchuensis Koidz. var. japonica (Makino) Hatus. ? | MAKS1096 |
| Stewartia monadelpha Siebold et Zucc. | MAKS0205, MAKS0206 |
| Stewartia pseudo-camellia Maxim. | MAKS0203, MAKS0204 |
| Streptopus streptopoides (Ledeb.) Frye et Rigg var. japonicus (Maxim.) Fassett | MAKS2151, MAKS2366 |
| Swertia bimaculata (Siebold et Zucc.) Hook. et Thoms. | MAKS1085 |
| Swertia japonica (Schult.) Makino | MAKS1082, MAKS1083 |
| Symplocarpus foetidus Nutt. var. latissimus (Makino) Hara | MAKS2111 |
| Symplocos chinensis (Lour.) Druce var. leucocarpa (Nakai) Ohwi f. pilosa (Nakai) Ohwi | MAKS1118, MAKS1119, MAKS1120, MAKS1121, MAKS1122 |
| Symplocos glauca (Thunb.) Koidz. | MAKS1126 |
| Symplocos lancifolia Siebold et Zucc. | MAKS0477, MAKS1127 |
| Symplocos lucida Siebold et Zucc. | MAKS1125 |
| Symplocos theophrastiifolia Siebold et Zucc. | MAKS1123, MAKS1124 |
| Syneilesis palmata (Thunb.) Maxim. | MAKS0569, MAKS0991 |
