An anime adaptation of Black Lagoon, produced by Madhouse, aired on Chiba TV from April 8, 2006 to June 24, 2006 for twelve episodes. A second season, labeled Black Lagoon: The Second Barrage and consisting of twelve more episodes, ran from October 3, 2006 to December 19, 2006. The second season focuses less on character development than the first season and more on the jobs they do. A five volume original video animation titled Black Lagoon: Roberta's Blood Trail was released in July 2010.
The anime was licensed in the United Kingdom and Australasia by Madman Entertainment. On July 3, 2008, Geneon Entertainment and Funimation Entertainment announced an agreement to distribute select titles in North America. While Geneon will still retain the license, Funimation will assume exclusive rights to the manufacturing, marketing, sales and distribution of select titles. Black Lagoon was one of several titles involved in the deal. Geneon's English dub premiered on G4 Canada on October 26, 2007 and Starz Edge began airing it on February 29, 2008 to American audiences. The series aired in Australia on the Sci Fi Channel.
The first season was released on six DVDs, each containing two episodes, between August and December 2006. The second season mirrored this, being released from January to June 2007. The Blu-ray Disc releases of the two seasons included a total of seven short omake specials, each no longer than five minutes, that depict the characters in various humorous situations. In 2010, the series was released in four, two for each season, boxsets from August to September.
Geneon's North American dub was released on three DVD compilations, each containing four episodes, between May 22 and September 18, 2007. After being released individually, with volume one having a limited edition version containing a steelbook box that comes with a bonus disc with slots for all 3 volumes, the boxset of the entire first season was released December 30, 2008. The fourth bonus disc, available in the season one box set or the volume one steelbook edition, has a 15 minute behind the scenes with the English crew and voice actors, the "Red Fraction" music video performed by Mell, promotional videos, the creditless opening and ending, and Japanese opening. The Second Barrage volumes were released in the same manner, with the box set released in North America on April 14, 2009, case with episodes 13–24 on three discs with English/Japanese audio and English subtitles. The box set/steelbook version bonus disc includes promotional videos and the creditless opening and ending. At Anime Expo 2010, Funimation announced their licensing of the Roberta's Blood Trail OVA, which was released in 2013. The first and second seasons were re-released on Blu-ray Disc/DVD combo pack on December 4, 2012.
The series returned to American television on the Funimation Channel on February 15, 2013. The anime has also aired in Italy on MTV Italy, in Sweden on ZTV and on Animax in Spain, Portugal and Germany.