The last section of Gulliver's Travels is partially a satire of race-relations in European society. It would have been easy to show the superior race as, for example, a darker-skinned race that Gulliver discovers ruling over whites, but that would have been obvious and too easy for a writer of Swift's skill. Instead, he uses a common beast of burden that no person thinks of as intelligent, the horse. Horses have been domesticated and used for labor for centuries, and to show them as the rulers of a Utopian society is to call into question every assumption of modern science. Gulliver is astonished, even ascribing the Houyhnhnm intelligence to magic, but quickly finds himself drawn into the Houyhnhnm's society of peace and non-conflict.
[I] wondered more to see the rest employed in domestic business... However, this confirmed my first opinion, that a people who could so far civilise brute animals, must needs excel in wisdom all the nations of the world.
(Swift, Gulliver's Travels, eNotes eText)
His assumption that a smart animal must have an even smarter human master is quickly corrected, and Gulliver discovers that he himself is considered to be little more than a smarter-than-average Yahoo. By changing all of Gulliver's preconceptions about how humans and animals interact, Swift challenged 18th century readers to examine their own prejudices and wonder if they are based in anything but societal norms and indoctrinated bias. A horse, as a creature that most people take for granted as domestic and used for human-centric goals, is a perfect metaphor for any assumptions that people make about other people, whether it be for their race, religion, or gender.
Interpretation of the Houyhnhnms has been vexatious. It is possible, for example, to regard them as a veiled criticism by Swift of the British Empire's treatment of non-whites as lesser humans, and it is similarly possible to regard Gulliver's preference (and immediate division of Houyhnhnms into color-based hierarchies) as absurd and the sign of his self-deception. In a modern context it can be seen as presenting an early example of animal rights concerns, especially in Gulliver's account of how horses are cruelly treated in his society and the reversal of roles, and a possible inspiration for Pierre Boulle's novel Planet of the Apes.
Gulliver's last voyage leads him to the island inhabited by the Houyhnhnms,horses endowednwith reason that rule over the Yahoos, a vile species of animals resembling human beings. Gulliver admires the superiority of the Houyhnhnms and is ashamed of his similarity with the Yahoos.