The specific name commemorates Heinrich Kühn, a German bird collector who worked for Ernst Hartert in Indonesia.

New analysis published in 2014 by Seán Kelly et al. proposed re-establishing the Wakatobi flowerpecker as a distinct species, based on DNA and morphological comparisons.

[1] This suggests that neither species can traverse the 27 kilometres (17 mi) between the Wakatobi islands and Sulawesi mainland.

Additionally, there are subtle color variations: compared to the grey-sided flowerpecker, male Wakatobi flowerpeckers have bluer upper feathers, lighter side feathers, and their red coloring extends further down.

[1] Although the area lies within the Wakatobi National Park, there is currently no environmental protection,[2] and scientists have expressed concern over its prospects given the rate of human development in the region.