Bleeker 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. He acquired many of his specimens from local fishermen, but he also built up an extended network of contacts who would send him specimens from various government outposts throughout the islands.
During his time in Indonesia, he collected well over 12,000 specimens, many of which currently reside at the Natural History Museum in Leiden.
After his return to the Netherlands in 1860, he started publishing the Atlas Ichthyologique, a comprehensive account of his studies done in Indonesia, featuring over 1,500 illustrations. It was published in 36 volumes between 1862 and his death in 1878. Between 1977 and 1983, the Smithsonian republished the work in 10 volumes.
Bleeker published more than 500 papers on ichthyology, describing 511 new genera and 1,925 new species.