Microexons exhibit striking evolutionary conservation and are subject to precise, switch-like regulation in neurons, orchestrated by the splicing factors
Srrm3
and
Srrm4
. Disruption of these regulators in mice leads to severe neurological phenotypes, and their misregulation is linked to human disease. However, the specific microexons involved in these phenotypes and the effects of individual microexon deletions on neurodevelopment, physiology, and behavior remain poorly understood. To explore this, we generated zebrafish lines with deletions of 18 individual microexons, alongside
srrm3
and
srrm4
mutant lines, and conducted comprehensive phenotypic analyses. We discovered that while loss of
srrm3
, alone or together with
srrm4
, resulted in significant alterations in neuritogenesis, locomotion, and social behavior, individual microexon deletions typically produced mild or no noticeable effects. Nonetheless, we identified specific microexons associated with defects in neuritogenesis (
evi5b
,
vav2
,
itsn1
,
src
) and social behavior (
vti1a
,
kif1b
). Additionally, microexon deletions triggered coordinated transcriptomic changes in neural pathways, suggesting the presence of molecular compensatory mechanisms. Our findings suggest that the severe phenotypes caused by
Srrm3/4
depletion arise from the combined effects of multiple subtle disruptions across various cellular pathways, which are individually well-tolerated.