The Japanese firm's annual contest is open to those photographs of tiny subjects taken down a microscope.
Of thousands of entrants from scientists and artists from across the globe, 71 were given special honours.
The zebrafish took first place, while second went to a series of snaps of a developing clownfish embryo.
Other images included an iridescent leaf roller weevil and the pollen-producing structures of a Hebe plant.
A fluorescent skeleton of a zebrafish, an adorable embryonic chameleon and the compound eye and feeding tube of a bogong moth are among the incredible close-ups that made the finals of Nikon's 'Small World' competition.
The Japanese firm's annual micrography competition — for images of tiny subjects taken down a microscope — has showcased the world's breath-taking fauna and fauna in a detail not visible to your naked eye.
First prize was awarded to the zebrafish — with a series of snaps of a developing clownfish embryo taking second and a colourful close up of a snail's tongue coming third.
The winning photograph was a stunning composite of a zebrafish with a fluorescent skeleton and vibrant blue scales, which was taken by one Daniel Castranova.
It was created by stacking 350 images on top of each other and painstakingly stitching them together.
The photograph is particularly significant as it shows the presence of lymphatic vessels inside the zebrafish's skull, which were previously thought to occur only in mammals.
The finding could revolutionise research into treatments for brain diseases — such cancer and Alzheimer's.
'The image is beautiful, but also shows how powerful the zebrafish can be as a model for the development of lymphatic vessels,' Mr Castranova said.
'Until 2015, we thought this type of lymphatic system only occurred in mammals.'
'By studying them now, the scientific community can expedite a range of research and clinical innovations — everything from drug trials to cancer treatments.'
'This is because fish are so much easier to raise and image than mammals.'
Second place was awarded to Daniel Knop for his incredible image of the embryonic development of a clownfish.
Mr Knop's series shows days one, three, five and nine of the clownfish's development using image-stacking.
The images allow viewers to see how the clownfish grow until just before it hatches.
In third place was a snap by Igor Siwanowicz, showing the colourful tongue of a freshwater snail.
Nikon Small World recognised 71 photos, out of thousands of entries from scientists and artists across the globe.