Two years later, he participated as assistant-naturalist in a fishery survey on the west coast of Ireland, organized by the Royal Dublin Society. This expedition was led by William Spotswood Green, with whom Holt would work together for much of his later career. That survey made Holt's name as an ichthyologist; he published not only several papers on the eggs and the early larval stages of fish but also wrote the general report of the expedition. As a result of Green's and Holt's work, the government instituted a formal program of fishery surveys under the auspice of the newly formed Congested Districts Board in 1892. Green became the board's Chief Inspector of Fisheries, while Holt participated as a scientific advisor, although he would leave Ireland for a few years.