To design effective conservation and management strategies at the national scale, it is important to consider population trends across space and time. Here we assessed the near threatened Rothschild's giraffe (Giraffa camelopardalis rothschildi) in Uganda. We applied individual-based photographic surveys to generate abundance estimates for all extant populations, using either mark-recapture estimates or complete enumeration, and reviewed available historical records to reconstruct the population history of giraffe in Uganda. Although anecdotal evidence from the early 20th century suggests giraffe were widely distributed and abundant, the earliest quantitative estimates from the 1960's suggest a countrywide population of nearly 1,800 individuals across five major populations. Between the 1960's and the 1990's, giraffe numbers in Uganda declined by approximately 90%; such that at the nadir in the early 1990's, there were fewer than 100 giraffe and three of five populations went locally extinct. Multiple lines of evidence attribute this decline to increased illegal hunting caused by widespread political and social instability. Populations rebounded from mid 1990's to the mid 2010's with current national estimates of approximately 1,400 adult/subadult individuals, mostly attributed to the growth of a single population in northern Murchison Falls National Park (MFNP). Our recent mark-recapture estimates for northern MFNP indicate the adult/subadult population size is 1,318 (±27.6 SE) giraffe - accounting for over 90% of the current total population in Uganda, thereby creating an “all the eggs in one basket” risk. Recent conservation measures by management authorities seek to spread this risk by translocating individuals from MFNP to several other locations to reinforce existing populations or create new populations. The increase in the northern MFNP giraffe population suggests that it can serve as a source for these translocations, and the understanding of historical distribution can be used to inform future reintroduction and reinforcement efforts.