Hydroxamate substituted azaindoline cyanine dyes, conjugates thereof and methods of using the same are provided. The subject cyanine dyes include an azaindoline ring having a hydroxamate substituent. The dyes may further include a reactive group moieties (RGM) and/or a water soluble group. Also provided are conjugates of the subject dyes. Also provided are tandem conjugates including a fluorescent protein capable of energy transfer to the dye. Methods of detecting an analyte in a sample by contacting the sample with a detection reagent are provided. The detection agent may be a dye-conjugate that specifically binds the analyte, or may be a reactive dye which conjugates to the analyte. Also provided are compositions, e.g., kits, etc., incorporating such dyes which facilitate use in such methods.