Evidence from scanning electron microscopy of seed coat surfaces and leaf flavonoid chemistry has provided new insights into the relationships of the problematical Chenopodium flabellifolium from San Martín Island, Baja California. The seed surface of C. flabellifolium is basically smooth and thus is essentially the same as members of the subsection Lejosperma of section Chenopodium. This feature distinguishes the species from the taxon that has commonly been considered its nearest relative, namely C. neomexicanum of subsection Cellulata, which has an alveolate seed surface. Leaf flavonoid chemistry also serves to separate C. flabellifolium and C. neomexicanum. Chenopodium flabellifolium has also been viewed as conspecific with C. inamoenum (= C. hians or C. leptophyllum) of subsection Lejosperma. While the seed surface indicates that C. flabellifolium is best treated as a member of this subsection, other morphological as well as chemical data suggest that its closets affinities within the subsection lie with C. fremontii. The leaves of the two species are essentially of the same shape and collectively differ strikingly from those of C. hians and C. leptophyllum. Leaf flavonoid chemistry indicates that C. flabellifolium is closer to C. fremontii than to other taxa of subsection Lejosperma occurring in the western United States because both contain kaempferol 3-O-glycosides, which have not been detected elsewhere. The two species differ consistently in that the former has the pericarp attached to the seed whereas it is separable from the seed in the latter.