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Abstract Mimulus laciniatus (syn. Erythranthe lacinata) is an annual plant endemic to the Sierra Nevada region of California. Mimulus laciniatus is notable for its specialized ecological niche, thriving in granite outcrops of alpine environments characterized by shallow soils that dry out rapidly as the snowpack is exhausted during season-ending droughts. Due to its narrow habitat range and sensitivity to environmental change, this species serves as an important model for studying adaptation and survival in marginal habitats. As part of the California Conservation Genomics Project, here we report the sequencing and assembly of a high-quality nuclear genome and chloroplast genome of M. laciniatus. The primary assembly is 309.96 Mb and consists of 104 scaffolds with a scaffold N50 of 20.99 Mb, a largest contig size of 24.29 Mb and a contig N50 of 11.09 Mb, The alternate haplotype assembly consists of 194 scaffolds spanning 213.84 Mb. BUSCO completeness of the primary assembly is 98.6%. This high quality genome adds a valuable resource to the expanding collection of sequenced genomes of the monkeyflowers (Mimulus sensu lato), which have become a model clade for studying ecological adaptation, speciation, and evolutionary genetics.