A series of new fluorescent labeling reagentsbased on sulfoindocyanine dyes has been developed. We describe the synthesis and propertiesof these reagents. They contain succinimidyl ester reactive groups and can be readily conjugated to antibodies, avidin, DNA, lipids, polymers, and other amino-groupcontaining materials. The labeling reagents are water soluble, pH insensitive, and show much reduced dye aggregation underlabeling conditions. One of the reagents, Cy3, can be excited with the 488-, 514-and 532-nm laser lines and is optimally excited with the 546-nm mercury arc line. Another, Cy5, can be excited with the 633-nm HeNe and 647-nm Kr laser lines available with many flow cytometers and confocal laser-scanning microscopes. New laser diodes emitting near 650 nm should also be excellent excitation sources for Cy5.