Henry George Flanagan, son of George Millin Flanagan and his wife Ann, received his schooling at the Public School, Komga. He became a farmer on Prospect Farm, in the Division of Komga, which he had acquired early in his career and where he lived for the rest of his life. In 1890 he married Florence Reynolds, who shared his work and hobbies. In February 1889 he started collecting plants with characteristic thoroughness, carefully selecting his specimens and taking great pains to ensure that they were well-preserved. In addition to building up a private collection he donated specimens to herbariums. For example, in 1891 he sent 57 splendidly preserved plant species to the Albany Museum in Grahamstown, followed by further specimens over the next ten years. The museum's director, botanist S. Schonland*, described him in 1895 as a collector "whose excellently prepared specimens again embraced a number of type-specimens and rare plants not previously represented in our collection". Another early collection was sent in 1892 to Peter MacOwan*, then government botanist in Cape Town, and was added to the Government Herbarium. MacOwan recognised him as a potentially valuable collector and provided help and encouragement.
At first Flanagan collected in the Komga area, building up the most complete record of its flora for many years to come, and thoroughly explored the Kei River valley to its mouth. A number of his beautifully preserved specimens were presented to the Royal Botanical Gardens at Kew, England, chiefly via his friend, Harry Bolus*. During November and December 1892 he made a collecting trip to Kimberley and collected around Hebron, Bethulie, Aliwal North, Burgersdorp and Molteno. A year later, from December 1893 to January 1894, the Flanagans, accompanied by Bolus, undertook a memorable collecting trip through Pondoland to the Free State, culminating in an ascent of Mont-aux-Sources. They were the first to properly explore the flora of the Lesotho mountains. The journey yielded an important collection of plants, which Flanagan donated to the Cape Government Herbarium that same year. It included Zaluzianskya flanaganii, found on the summit of Mount-aux-Sources, Erica flanaganii, and the beautiful Impatiens flanaganiae, named after Florence Flanagan who discovered it at Port St. Johns.
In April and May 1906 Flanagan visited Zimbabwe and collected some plants there. However, after 1895 he turned his attention mainly to the marine algae of the Eastern Cape coast. In 1898 he contributed a fine series of Eastern Cape algae to the Government Herbarium. During the same year he presented a collection of algae made at Robben Island and at Cape Morgan (on the Eastern Cape coast) to the Albany Museum. It contained some 50 species not yet represented in the museum's herbarium. Although his collecting activity gradually declined, he retained an interest in his private collection; for example, he received a parcel of duplicates from H.H.W. Pearson* of the South African Museum in 1908.
Flanagan was elected a Fellow of the Linnean Society in 1898. He became a member of the South African Association for the Advancement of Science in 1902, shortly after its formation, and remained a member for the rest of his life. During the latter part of his life he developed a beautiful garden on Prospect Farm, containing many rare trees, shrubs and succulents, both indigenous and exotic. Meanwhile he was a leading farmer of his district, and as a partner in the firm Flanagan Brothers participated in the development of a famous citrus farm. He was a modest person and had the misfortune of suffering from extended bouts of severe headache, probably migraine. His herbarium and botanical books were left to the Division of Botany of the Department of Agriculture and thus became part of the National Herbarium in Pretoria. The plants in his garden were bequeathed to the South African Government and were brought to Pretoria and planted at the Union Buildings, in an area named the Flanagan Arboretum. He was commemorated in the names of a number of species in addition to those already mentioned, including Gladiolus flanaganii, Protea flanaganii, Selago flanaganii, Cyrtanthus flanaganii, Raphionacme flanaganii and Bryopsis flanaganii.