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Although first isolated in 1889 and again in 1899 by scientists at Guinness, the discovery of ''Brettanomyces'' was first publicly published by Hjelte Claussen in 1904 after he cultured it in 1903 from English beers that exhibited a sluggish secondary fermentation <ref>[http://barclayperkins.blogspot.com/2013/06/when-was-brettanomyces-discovererd.html "When was Brettanomyces discovererd?" Ron Pattenson. Shut Up About Barclay Perkins blog. 06/29/2013. retrieved 08/18/2016.]</ref>. At the time of discovery, Claussen was aiming to recreate the flavor profile of traditional English ales by fermenting them with pure cultures of ''Saccharomyces'', and either pitching pure cultures of his newly discovered ''Brettanomyces'' yeast along with ''Saccharomyces'', or as he preferred, after the primary fermentation of ''Saccharomyces'' <ref>[https://www.facebook.com/download/448702618652516/GB190328184A.pdf "Improvements in and connected with the Manufacture of English Beers or Malt Liquors and in the Production of Pure Yeast Cultures for use therein." Patent application by Hjelte Claussen for ''Brettanomyces''. A.D. 1903.]</ref>. Although Claussen saw the character from ''Brettanomyces'' as a desirable character in ales and identified its character as a quality of traditional English ales, at some point ''Brettanomyces'' became identified as a contaminate in wineries and breweries due to some of the phenols, acids, and haze that it sometimes produces. These phenols and acids have generally been described as "barnyard", "burnt plastic", "wet animal", "fecal", and "horse sweat", although some tasters describe these flavors with different terminology because they percieve perceive certain flavor compounds differently while some other tasters simply cannot detect certain flavor compounds at all <ref name="smith_divol_2016"></ref><ref name="Schifferdecker">[http://onlinelibrary.wiley.com/doi/10.1002/yea.3023/pdf The wine and beer yeast Dekkera bruxellensis. Anna Judith Schifferdecker, Sofia Dashko, Olena P. Ishchuk, and Jure Piškur. 7 July 201.]</ref><ref name="Lucy_2015">[http://www.ajevonline.org/content/66/3/379 Brettanomyces bruxellensis Aroma-Active Compounds Determined by SPME GC-MS Olfactory Analysis. C.M. Lucy Joseph, Elizabeth A. Albino, Susan E. Ebeler, Linda F. Bisson. 2015.]</ref>. The general viewpoint of brewers (other than Lambic and Flanders red/brown brewers in Belgium) and vintners that ''Brettanomyces'' is primarily a spoilage organism held for many decades, and still holds in most cases. More recently the positive flavor components that have been identified in ''Brettanomyces'' beer such as pineapple, stone fruits, and to some degree acetic acid, have regained popularity with brewers outside of Belgium. Wine tasters have also described wines with certain flavor compounds derived from ''Brettanomyces'' as positive characteristics of wine. It is important to keep in mind that individual tasters on tasting panels describe some flavor compounds as "negative" while others describe them as "positive" (and sometimes a mixed response is given by a taster in regards to a certain flavor compound), and this discrepancy in interpretations of ''Brettanomyces'' derived flavor compounds appears to be based on personal preference and experience. In some cases, for example for vinyl phenols, low levels that are not detectable by some people, but detected by others contributes contribute positively to wine, while higher amounts contribute negatively. Thus, lower intensity of some flavor compounds can be seen as more desirable. Overall, the enjoyment or displeasure of the various flavor compounds produced by ''Brettanomyces'' and at certain levels is completely subjective <ref name="Lucy_2015" />.

Recently a new species of ''Brettanomyces'' has been proposed, although classification has not been fully established. The proposed name is ''Brettanomyces acidodurans'' sp. nov. Two strains of ''B. acidodurans'' were isolated from olive oil from Span and Israel, however, its presence in olive oil has been described as "rare" because only two strains were found after searching dozens of olive oils. Its closest relation is to ''B. naardenesis'' by 73% of its genetic makeup. No telemorph teleomorph form was observed. This species is a strong acetic acid producer, and it is very tolerant of acetic acid in its environment. It can consume lactose and cellobiose, but does not consume maltose. it is unknown but a possibility that this species contributes to the vinegary taste of spoiled olive oils, although this has generally been attributed to acetic acid bacteria <ref>[https://www.ncbi.nlm.nih.gov/pubmed/28160110 Brettanomyces acidodurans sp. nov., a new acetic acid producing yeast species from olive oil. Péter G, Dlauchy D, Tóbiás A, Fülöp L, Podgoršek M, Čadež N. 2017.]</ref>.

''Brettanomyces'' is commonly isolated from the surface of wood structures within breweries, wineries, and sometimes cideries. These include structures such as wooden fermentation vessels, walls of the building, as well as the inside surface of wood barrels and actually buried within the wood of barrels up to 8 mm, with the highest concentration of surviving cells being at the top staves where oxygen is more accessible. Some strains are able to utilize the cellulose of the wood as a carbon source. Ozone has been shown to be an effective way to kill ''Brettanomyces'' that is buried in the wood of oak barrels, but the ozone must be applied for an adequate time to allow for he the ozone to diffuse into the oak. Heating the entirety of the oak barrels to 60°C for 20 minutes with hot water has also been found to be an effective way of killing ''Brettanomyces'' within the wood of barrels <ref name="Agnolucci_2017" />. Although the role of ''Brettanomyces'' appears to be limited in distillation, it has been isolated during the fermentation process of tequila making. It has also been isolated from drains, pumps, transfer hoses, and other equipment that is difficult to sanitize. The survivability of ''Brettanomyces'' has also partly been attributed to its ability to form a [https://en.wikipedia.org/wiki/Biofilm biofilm] (in particular ''B. bruxellensis''). Microorganisms that can form a biofilm are more resistant to chemical cleaning agents and sanitizers than those that don't. ''Brettanomyces'' has therefore been identified as a significant contaminate for breweries and wineries. Oak barrels from wineries with unsanitary practices , in particular , have been identified as common contamination sites for ''B. bruxellensis''. ''Brettanomyces'' is also commonly found in sherry, and is found (although only rarely) in olive production, lemonade, kombucha, yogurt, pickles, and soft drinks. ''B. anomalus'' and ''B. bruxellensis'' are generally found much more commonly than the other three species of ''Brettanomyces''. <ref name="smith_divol_2016">[http://www.sciencedirect.com/science/article/pii/S0740002016302659 Brettanomyces bruxellensis, a survivalist prepared for the wine apocalypse and other beverages. Brendan D. Smith, Benoit Divol. June 2016.]</ref>.