| Origin | Code | Comment | Supplementary Taxo |
| Lachnoanaerobaculum gingivalis | ISLgi | | |
| Lactobacillus acetotolerans | ISLaac | | |
| Lactobacillus acidophilus | ISLac | | |
| Lactobacillus casei | ISLca | | |
| Lactobacillus crispatus | ISLcr | | |
| Lactobacillus delbrueckii | ISLde | | |
| Lactobacillus fructivorans | ISLfr | | |
| Lactobacillus gasseri | ISLga | | |
| Lactobacillus helveticus | ISLhe | | |
| Lactobacillus heterohiochii | ISLahe | | |
| Lactobacillus hokkaidonensis | ISLho | | |
| Lactobacillus johnsonii | ISLjo | | |
| Lactobacillus kefiranofaciens | ISLke | | |
| Lactobacillus plantarum | ISLpl | | |
| Lactobacillus reuteri | ISLre | | |
| Lactobacillus rhamnosus | ISLrh | | |
| Lactobacillus sakei | ISLsa | | |
| Lactobacillus salivarius | ISLasa | | |
| Lactococcus garvieae | ISLgar | | |
| Lactococcus lactis | ISLla | | |
| Leclercia adcarboxglata | ISLead | | |
| Leclercia adecarboxylata | ISLad | | |
| Leeuwenhoekiella blandensis | ISLbl | | |
| Legionella drancourtii | ISLdr | | |
| Legionella longbeachae | ISLlo | | |
| Legionella pneumophila | ISLpn | | |
| Leifsonia sp. | ISLfsp | | |
| Leifsonia xyli | ISLxx | Predefined common nomenclature | |
| Leifsonia xyli subsp. cynodontis | ISLxc | Predefined common nomenclature | |
| Lelliottia amnigena | ISLam | | |
| Lentimicrobium saccharophilum | ISLesa | | |
| Lentisphaera araneosa | ISLar | | |
| Leptolyngbya sp. | ISLesp | | |
| Leptonema illini | ISLil | | |
| Leptospira biflexa | ISLbi | | |
| Leptospira borgpetersenii | ISLbp | Predefined common nomenclature | |
| Leptospira interrogans | ISLin | | |
| Leptospirillum ferrodiazotrophum | ISLfe | | |
| Leptospirillum ferrooxidans | ISLefe | | |
| Leptospirillum rubarum | ISLru | | |
| Leptospirillum sp. | ISLsp | | |
| Leptotrichia buccalis | ISLbu | | |
| Leucaena diversifolia | ISLdi | | |
| Leuconostoc lactis | ISLela | | |
| Leuconostoc mesenteroides | ISLme | | |
| Levybacteria bacterium | ISLba | | Candidatus Levybacteria bacterium |
| Limnohabitans sp. | ISLisp | | |
| Listeria grayi | ISLgr | | |
| Listeria ivanovii | ISLiv | | |
| Listeria monocytogenes | ISLmo | | |
| Listeria seeligeri | ISLse | | |
| Listeria welshimeri | ISLwe | | |
| Loktanella vestfoldensis | ISLve | | |
| Lonsdalea britannica | ISLbr | | |
| Lyngbya sp. | ISLysp | | |
| Lysobacter gummosus | ISLgu | | |