Sporophytes and gametophytes of Equisetum arvense, E. laevigatum, and E. telmateia were analyzed using enzyme electrophoresis to estimate isozyme number. Despite their uniformly high chromosome numbers (2n = 216), these three species exhibited isozyme numbers typical of diploid seed plants for the enzymes AAT, ADH, ALD, GDH, [NADP]IDH, LAP, MDH, [NADP]ME, PGI, PGM, SkDH, and 6PGDH. All three species exhibited an additional isozyme for TPI. There is, therefore, no genetic evidence for low base numbers such as x = 9 and x = 12 suggested for Equisetum. Intact chloroplasts were isolated from E. arvense and the chloroplast extract compared electrophoretically to whole plant extracts. The single enzymes observed for LAP, GDH, [NADP]IDH, and [NADP]ME were absent from the chloroplast extract. Isozymes AAT‐1, ALD‐2, MDH‐3, PGI‐1, PGM‐2, SkDH‐2, 6PGDH‐2, TPI‐2, and TPI‐3 were active in the chloroplast fraction; 6PGDH‐1, PGI‐2, PGM‐1, and TPI‐1 were lacking from the chloroplast fraction and were considered cytosolic. Isozymes AAT‐2, MDH‐1, MDH‐2, MDH‐4, and SkDH‐1 were also lacking from the chloroplast fraction but because AAT, MDH, and SkDH have been reported from several subcellular compartments, their localization is unknown. These findings indicate that isozymes in Equisetum species are subcellularly compartmentalized as has also been demonstrated for homosporous ferns, gymnosperms, and angiosperms.