Micromammals are abundant in nature and have a significant role as reservoirs for various parasites and pathogens. Very little is currently known about Sarcocystis prevalence and species richness in wild micromammals from Mediterranean Spain. In the present study, a pool of heart, lungs, and brain of 371 individuals representing three species, Algerian mouse (Mus spretus), wood mouse (Apodemus sylvaticus), and white-toothed shrew (Crocidura russula), was screened for Sarcocystis using molecular methods. Animals were sampled across 4 seasons in both natural and agricultural habitats. Prevalence in white-toothed shrew (28%) was significantly higher than in wood and Algerian mouse (17% and 18%, respectively). The lowest prevalence occurred in autumn, whereas no significant differences were detected between habitats. Analysis of 28S rRNA sequences revealed 11 Sarcocystis lineages, with the highest lineage diversity observed in the Algerian mouse. Based on comparative sequence and phylogenetic analysis, most of these lineages are suspected to use snakes as definitive hosts (DHs), three are associated with birds, and the DHs for two lineages are likely mammals. Notably, cox1 sequences could not be used to confidently identify all lineages. Our results reveal substantial diversity of Sarcocystis in Mediterranean micromammals and provide new insights into their transmission cycles.