Over 50 magnetic bottom depths derived from spectra of magnetic anomalies in Eastern Egypt along the Red Sea margin show variable magnetic bottoms ranging from 10 to 34 km. The deep magnetic bottoms correspond more closely to the Moho depth in the region, and not the depth of 580 °C, which lies significantly deeper on the steady state geotherms. These results support the idea of Wasilewski and coworkers that the Moho is a magnetic boundary in continental regions. Reduced-to-pole magnetic highs correspond to areas of Younger Granites that were emplaced toward the end of the Precambrian. Other crystalline Precambrian units formed earlier during the closure of ocean basins are not strongly magnetic. In the north, magnetic bottoms are shallow (10–15 km) in regions with a high proportion of these Younger Granites. In the south, the shoaling of the magnetic bottom associated with the Younger Granites appears to be restricted to the Aswan and Ras Banas regions. Complexity in the variation of magnetic bottom depths may arise due to a combination of factors: i) regions of Younger (Precambrian) Granites with high magnetite content in the upper crust, leaving behind low Curie temperature titanomagnetite components in the middle and lower crust, ii) rise in the depth of 580 °C isotherm where the crust may have been heated due to initiation of intense magmatism at the time of the Red Sea rifting (~ 20 Ma), and iii) the contrast of the above two factors with respect to the neighboring regions where the Moho and/or Curie temperature truncates lithospheric ferromagnetism. Estimates of fractal and centroid magnetic bottoms in the oceanic regions of the Red Sea are significantly below the Moho in places suggesting that oceanic uppermost mantle may be serpentinized to the depth of 15–30 km in those regions.