In this paper the focus is on the implementation of Photonis MCP-PMTs with single photon counting capability for LIDAR applications. In particular we are presenting our MCP-PMTs based on HI-QE photocathodes optimized for different spectral ranges (UV, Blue, Green with typical QE>30%) and for fixed laser wavelength of 355 nm and 532 nm [1]. In addition to the high QE, those photocathodes demonstrate low dark rates, typically below 50 Hz/cm 2 , property that is important for low-rate signal detection. The collection efficiency of the MCP is also improved to reach almost 100%, allowing to increase the detective QE by a factor of 1.5 compared to conventional MCP-PMTs [2]. The timing performance for MCP-PMTs operated at low and high rate photon fluxes are also studied. Non-linearity effects for high rate of illumination are analyzed and MCP-PMTs with extended linearity are presented. All these improved detection properties can be combined with the possibility of fast triggering and extended life time technology making these devices unique for future atmospheric and altimetry LIDAR missions.