A well isolation trenches for a CMOS device and the method for forming the same. The CMOS device includes (a) a semiconductor substrate, (b) a P well and an N well in the semiconductor substrate, (c) a well isolation region sandwiched between and in direct physical contact with the P well and the N well. The P well comprises a first shallow trench isolation (STI) region, and the N well comprises a second STI region. A bottom surface of the well isolation region is at a lower level than bottom surfaces of the first and second STI regions. When going from top to bottom of the well isolation region, an area of a horizontal cross section of the well isolation region is an essentially continuous function.