G-protein-coupled receptors (GPCRs) play fundamental roles in regulating various physiological processes as well as the activity of virtually all cells. Different GPCR families are responsible for different functions. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop an automated method to address the two problems: given the sequence of a query protein, can we identify whether it is a GPCR? If it is, what family class does it belong to? Here, a two-layer ensemble classifier called GPCR-GIA was proposed by introducing a novel scale called ‘grey incident degree’. The overall success rate by GPCR-GIA in identifying GPCR and non-GPCR was about 95%, and that in identifying the GPCRs among their nine family classes was about 80%. These rates were obtained by the jackknife cross-validation tests on the stringent benchmark data sets where none of the proteins has ≥50% pairwise sequence identity to any other in a same class. Moreover, a user-friendly web-server was established at http://218.65.61.89:8080/bioinfo/GPCR-GIA. For user's convenience, a step-by-step guide on how to use the GPCR-GIA web server is provided. Generally speaking, one can get the desired two-level results in around 10 s for a query protein sequence of 300–400 amino acids; the longer the sequence is, the more time that is needed.