Stearyl coenzyme A desaturase (SCD), also known as delta-9 desaturase, catalyzes the rate-limiting step in the formation of monounsaturated fatty acids. In mammals, depletion or inhibition of SCD activity generally leads to a decrease in triglycerides and cholesteryl esters. However, the endogenous role of
scd
in teleost fish remains unknown. Here, we generated a zebrafish
scd
mutant (
scd
-/-
) to elucidate the role of
scd
in lipid metabolism and sexual development. Gas chromatography-mass spectrometry (GC-MS) showed that the
scd
-/-
mutants had increased levels of saturated fatty acids C16:0 and C18:0, and decreased levels of monounsaturated fatty acids C16:1 and C18:1. The mutant fish displayed a short stature and an enlarged abdomen during development. Unlike
Scd
-/-
mammals, the
scd
-/-
zebrafish showed significantly increased fat accumulation in the whole body, especially in the liver, leading to hepatic mitochondrial dysfunction and severe cell apoptosis. Mechanistically,
srebf1
, a gene encoding a transcriptional activator related to adipogenesis,
acc1
and
acaca
, genes involved in fatty acid synthesis, and
dgat2
, a key gene involved in triglyceride synthesis, were significantly upregulated in mutant livers to activate fatty acid biosynthesis and adipogenesis. The
scd
-/-
males exhibited defective natural mating behavior due to defective genital papillae but possessed functional mature sperm. All defects in the
scd
-/-
mutants could be rescued by ubiquitous transgenic overexpression of
scd
. In conclusion, our study demonstrates that
scd
is indispensable for maintaining lipid homeostasis and development of secondary sexual characteristics in zebrafish.