from qgis.gui import QgsMessageBar

input_layers = []
layers = iface.legendInterface().layers()
for layer in layers:
  if layer.type() == QgsMapLayer.RasterLayer:
     input_layers.append(layer)

pcs_list = []
for input in input_layers:
  pcs_list.append(input)
  pcs_str = list(set([pcs.crs().authid() for pcs in pcs_list]))

text = "You have multiple layers with different CRS in this project: " + str(pcs_str).translate(None, "[]u")

if len(pcs_str) >1:
    iface.messageBar().pushMessage("Alert",text, level=QgsMessageBar.WARNING,duration=20)
else:
  pass

QgsMapLayerRegistry.instance().legendLayersAdded.connect(myF‌​unc)