John Ernest Holloway was born in Christchurch on 12 February 1881, the son of John Holloway, a bank manager, and his wife, Anna Thorpe. As a child he was influenced by his father, who was a keen churchman, amateur naturalist and microscopist. He attended the Bishop's School from 1891 to 1895 and Nelson College from 1895 to 1900. The following year he went to Auckland, entering St John's College to prepare for the Anglican priesthood and enrolling at Auckland University College as a science student. There, A. P. W. Thomas, professor of natural science, interested him in primitive ferns and he completed an MSc degree with first-class honours in 1905. His thesis dealt with the anatomy of native club-mosses. Two years later he passed the examination for licentiate in theology. He was ordained in 1908 and his first curacies were in Hawera and Wanganui.
On 21 July 1908, at Christchurch, he married Margaret Brenda North, whose father was a rector in Shropshire. In 1909 the couple visited Margaret's family there, and stayed on in England for two years. John gained some experience of slum parishes in London, but was based mainly at Barnsley, Yorkshire, where his botanical interests were stimulated by encountering coal balls containing carboniferous plants.
After his return to New Zealand Holloway experienced his most productive period in botanical research, while simultaneously carrying out his duties as vicar at East Oxford (1912–16), Hokitika (1916–21) and Leeston (1922–24). He continued and extended his MSc work on Lycopodium, and began research on Tmesipteris and Hymenophyllaceae, writing two important papers as a result. Oxford was handy to Christchurch, but Hokitika was the promised land to a student of ferns. His motor-cycle served both science and parishioners well. Mid-week he would take a sleeping bag and spend a day and a night in the laboratory of Charles Chilton, professor of biology. His correspondence with fellow researchers in New Zealand (especially Leonard Cockayne) and abroad countered the isolation. His parishioners bought him apparatus that would save him from travelling and presented him with the robes he needed to receive his DSc from the University of New Zealand in 1917.
In 1921 John Holloway became a fellow of the New Zealand Institute (later the Royal Society of New Zealand); in 1920 he received the Hutton Memorial Medal and in 1930 the Hector Memorial Medal and Prize. In 1923 he succeeded Winifred Aitken (formerly Betts), who retired from the lectureship in botany at the University of Otago when she went to Scotland with her husband. Holloway regretfully gave up most of his parish work, although he continued to wear a clerical collar, occasionally preaching in the cathedral or filling in for a colleague.
He was ill-prepared for the task that lay ahead. In his work at the university John Holloway received no assistance, even with practical classes. The botany department was a single room with a corner partitioned to serve as an office. A small garden included a glasshouse, a Moeraki boulder and a urinal. Economies were necessary. A substantial part of the annual allowance for equipment and material (about £50) remained unspent: Holloway maintained that the full sum could not be used while the working space and lack of assistance were such limiting factors. For microscopy, which dominated the practical work, lamps were made from cocoa tins and simple mirrors sufficed below the microscope stage. Degree classes were small, with usually 10 to 15 beginners, of whom fewer than half would undertake a second or third year; the honours class never had more than three students. There were Saturday classes and field trips and kindly teachers like Holloway offered some hospitality at home. Seven of Holloway's honours students were to become professional botanists, the most distinguished being his son, Jack, who was to become New Zealand's foremost forest ecologist and an honorary Otago DSc, and Dame Ella Campbell, who was honoured for research on lower plants that she began under Holloway's direction.
Imbued with a spirit of service, Holloway catered first to the needs of his students, but between 1930 and 1944 he published nine papers, five on ferns. Through his early work on club-mosses Holloway had become aware of the evolutionary significance of primitive ferns, and his work in this field attracted international interest. The most primitive of all ferns, Tmesipteris, grew abundantly in Westland forests and its life cycle was still largely mysterious. This was because the crucial reproductive stage was uncommon and hard to recognise among so much else resembling it in colour, size and shape. Exercising patience, diligence, and his powers of interpretation, Holloway closed a major gap in knowledge.
John Holloway was elected a fellow of the Royal Society of London in 1937. Otago University recognised this honour by changing his title to lecturer-in-charge and allowing him to retain Campbell, a recent honours graduate, as his assistant. In 1939 he paid a brief visit to scientists with whom he had corresponded in America and Britain. His health was declining, however, and in 1944 he retired. Within a year, on 6 September 1945 at Timaru, he died, survived by three daughters and two sons. His wife, Margaret, had died the previous year. The Council of the University of Otago minuted that he had been 'an inspiring teacher and guide' and that 'His investigations have thrown a flood of light on the origin and relationships of primitive land plants.'