Blastocystis is a ubiquitous intestinal protist that infects a broad range of vertebrate hosts, including equines. In this study, we characterized the prevalence, associated risk factors, and subtype diversity of Blastocystis sp. in fecal samples from five equine species (horses, donkeys, ponies, mules, and a zebra) collected from four Algerian provinces between December 2021 and December 2022. Of 197 fecal samples examined using microscopy and probe-based quantitative PCR (qPCR), 74 (37.6%) were positive for Blastocystis sp. Univariate analysis revealed significant associations between Blastocystis detection and equine species (p = 0.009), breeding system (p = 0.039), and climate zone (p = 0.045): horses (45.2%, 47/104) had a higher detection rate than donkeys (27.0%, 24/89), and animals raised under intensive systems (55.3%, 21/38) were more frequently positive than those in semi-extensive (36.7%, 11/30) or extensive (32.6%, 42/129) systems. Detection rates were higher in semi-arid (48.7%) and humid (30.6%) zones than in arid (25.0%) and sub-humid (15.8%) zones. No variable retained independent significance in the multivariable logistic regression analysis. Subtype determination was performed by nested PCR and Sanger sequencing of the SSU rRNA gene. Among 25 sequences of sufficient quality for subtype assignment, seven subtypes were identified: ST1 (n = 3, 12%), ST2 (n = 3, 12%), ST3 (n = 3, 12%), ST4 (n = 9, 36%), ST10 (n = 3, 12%), ST24 (n = 1, 4%), and ST33 (n = 3, 12%). Two additional sequences displayed polymorphisms consistent with ST48 but were too short for definitive assignment (ST48-like). Horses harboured subtypes ST1–ST4, ST10, ST33, and ST48-like; donkeys harboured ST1, ST2, ST4, ST24, ST33, and ST48-like; and ST10 was identified in mule and zebra samples. This is the first molecular survey of Blastocystis sp. in equines from Algeria and reveals the presence of zoonotic subtypes (ST1–ST4) alongside the putatively equid-associated subtype ST33, underscoring the importance of investigating equines as potential reservoirs under a One Health umbrella.