Fragile-X mental retardation autosomal homolog-1 (FXR1) is a muscle-enriched RNA-binding protein. FXR1 depletion is perinatally lethal in mice, Xenopus, and zebrafish; however, the mechanisms driving these phenotypes remain unclear. The FXR1 gene undergoes alternative splicing, producing multiple protein isoforms and missplicing has been implicated in disease. Furthermore, mutations that cause frameshifts in muscle-specific isoforms result in congenital multi-minicore myopathy. We observed that FXR1 alternative splicing is pronounced in the serine and arginine-rich intrinsicallydisordered domain; these domains are known to promote biomolecular condensation.Here, we show that tissue-specific splicing of fxr1 is required for Xenopus development and alters the disordered domain of FXR1. FXR1 isoforms vary in the formation of RNAdependent biomolecular condensates in cells and in vitro. This work shows that regulation of tissue-specific splicing can influence FXR1 condensates in muscle development and how mis-splicing promotes disease. KEYWORDS FXR1, alternative splicing, biomolecular condensation, myogenesis, Xenopus, muscle HIGHLIGHTS • The muscle-specific exon 15 impacts FXR1 functions • Alternative splicing of FXR1 is tissue-and developmental stage specific • FXR1 forms RNA-dependent condensates • Splicing regulation changes FXR1 condensate properties