He was employed as a medical officer in the Dutch East Indian Army from 1842 to 1860, stationed in Indonesia. During that time, he did most of his ichthyology work, besides his duties in the army. Many of his specimen he got from local fishermen, but he also built up an extended network of contacts who would send him specimen from various government outposts throughout the islands.
Subsequent to his return to the Netherlands in 1860, he started publishing his Altlas Ichthyologique, a comprehensive account of his studies done in Indonesia with over 1500 illustrations. It was published in 36 volumes between 1862 and Bleeker's death in 1878, and has been republished by the Smithsonian between 1977 and 1983 in 10 volumes.