Due to the difficulty in accurately identifying structural variants (SVs) across genomes, their impact on
cis
-regulatory divergence of closely related species, especially fish, remains to be explored. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood.
Siniperca chuatsi
and
S. scherzeri
are closely related but divergent in several phenotypic traits, making them an ideal model to study
cis
-regulatory evolution in sister species. Here, we generated chromosome-level genomes of
S. chuatsi
and
S. scherzeri
, with assembled genome sizes of 716.35 and 740.54 Mb, respectively. The evolutionary histories of
S. chuatsi
and
S. scherzeri
were studied by inferring dynamic changes in ancestral population sizes. To explore the genetic basis of adaptation in
S. chuatsi
and
S. scherzeri
, we performed gene family expansion and contraction analysis and identified positively selected genes (PSGs). To investigate the role of SVs in
cis
-regulatory divergence of closely related fish species, we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of
S. chuatsi
and
S. scherzeri
. Integrated analysis revealed that
cis
-regulatory divergence caused by SVs played an essential role in phenotypic divergence between
S. chuatsi
and
S. scherzeri
. Additionally, divergent broad H3K4me3 domains were mostly associated with cancer-related genes in
S. chuatsi
and
S. scherzeri
and contributed to their phenotypic divergence.