We noted a cluster of 4 cases of infection or colonization by Emericella spp., identified by sequence-based analysis as E. quadrilineata. Sequence-based analysis of an international collection of 33 Emericella isolates identified 12 as E. nidulans, all 12 of which had previously been identified by morphologic methods as E. nidulans. For 12 isolates classified as E. quadrilineata, only 6 had been previously identified accordingly. E. nidulans was less susceptible than E. quadrilineata to amphotericin B (median MICs 2.5 and 0.5 mg/L, respectively, p<0.05); E. quadrilineata was less susceptible than E. nidulans to caspofungin (median MICs, 1.83 and 0.32 mg/L, respectively, p<0.05). These data indicate that sequence-based identification is more accurate than morphologic examination for identifying Emericella spp. and that correct species demarcation and in vitro susceptibility testing may affect patient management.