Methods for electrophoretic karyotyping of filamentous fungi in the genus Trichoderma were developed. These techniques permitted the separation and visualization of intact chromosomes from viable protoplasts. Three strains were analyzed: Trichoderma harzianum strains T12 his-2 and T95 lys-1, and a prototrophic strain (1295-22) produced by protoplast fusion of T12 his-2 with T95 lys-1. Four chromosome bands ranging in size from 2.2 Mb (megabase pairs) to 5.4 Mb were visualized with strain T95 lys-1, whereas two chromosome bands were visualized for strains T12 his-2 and 1295-22. The largest chromosome of all three strains seems to be similar in size and has been estimated to be approximately 5.4 Mb. All remaining chromosomes observed were dissimilar in size. Methods for protoplast isolation, protoplast embedding, and electrophoretic conditions useful for separation of intact chromosomes ranging in size from 50 kb (kilobase pairs) up to approximately 6.0 Mb utilizing transverse alternating field electrophoresis (TAFE) will be discussed. The techniques provided should be applicable to a variety of lower eukaryotic organisms when using the TAFE system.