The coordination of the hypoxic response is attributed, in part, to hypoxia-inducible factor 1α (Hif-1α), a regulator of hypoxia-induced transcription. After the teleost-specific genome duplication, most teleost fishes lost the duplicate copy of Hif-1α, except species in the cyprinid lineage that retained both paralogues of Hif-1α (Hif1aa and Hif1ab). Little is known about the contribution of Hif-1α, and specifically of each paralogue, to hypoxia tolerance. Here, we examined hypoxia tolerance in wild-type (Hif1aa
+/+
ab
+/+
) and Hif-1α knockout lines (Hif1aa
−/−
; Hif1ab
−/−
; Hif1aa
−/−
ab
−/−
) of zebrafish (
Danio rerio
). Critical O
2
tension (
P
crit
; the partial pressure of oxygen (PO
2
) at which O
2
consumption can no longer be maintained) and time to loss of equilibrium (LOE), two indices of hypoxia tolerance, were assessed in larvae and adults. Knockout of both paralogues significantly increased
P
crit
(decreased hypoxia tolerance) in larval fish. Prior exposure of larvae to hypoxia decreased
P
crit
in wild-type fish, an effect mediated by the Hif1aa paralogue. In adults, individuals with a knockout of either paralogue exhibited significantly decreased time to LOE but no difference in
P
crit
. Together, these results demonstrate that in zebrafish, tolerance to hypoxia and improved hypoxia tolerance after pre-exposure to hypoxia (pre-conditioning) are mediated, at least in part, by Hif-1α.