The average yearly property tax paid by San Diego County residents amounts to about 3.47% of their yearly income. San Diego County is ranked 385th of the 3143 counties for property taxes as a percentage of median income. You can use the California property tax map to the left to compare San Diego County's property tax to other counties in California. Marin County collects the highest property tax in California, levying an average of $5,500.00 (0.63% of median home value) yearly in property taxes, while Modoc County has the lowest property tax in the state, collecting an average tax of $953.00 (0.6% of median home value) per year.