The method of labeling a sugar chain from a biological sample employs a single reaction vessel for the sequential performance of the following steps of (a) isolating a sugar chain from a sample using a sugar-trapping substance; (b) washing the sugar-trapping substance having the sugar chains trapped thereon; (c) releasing the sugar chain from the sugar-trapping substance; and (d) labeling the released sugar chain with UV/visible or fluorescent compound having an amino group forming a stable labeled sugar in fewer steps than a conventional ion exchange based technique.