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The following official despatch of General Persifor F. Smith, contains an opinion of the position of San Francisco totally different from that of the numerous California tourists. It is a valuable opinion, nevertheless, and led to the selection of the town of Benicia, on the Straits of Karquinez, as a military and naval station.

Headquarters Third Division,
San Francisco, April 5, 1849.

General:—Since my last communication no troops have arrived to change the strength of the force here; but the steam transport Edith arrived on the 21st of March, and reports that the transports Iowa and Massachusetts, the former having General Riley with a part of the 2d infantry, and the latter having the command of artillery for Oregon on board, left Valparaiso about the 8th of February. The former is expected here every day, and the Edith is held in readiness to convey the troops south to the position they are to occupy.

There will be great difficulty in establishing and maintaining a post at the mouth of the Gila, until more knowledge is acquired of the navigation of the head of the gulf of California and the lower part of the Colorado. Transportation by land from San Diego is impossible for large quantities of stores.

In the gulf, the winds blow in the winter almost invariably from the northward; and in the summer, when they come occasionally from southward, it is in violent gales, with severe squalls and thunder, rendering it very dangerous to be in the gulf then. In other words, it is always difficult to run up the gulf, but almost always easy to run south. These circumstances render the employment of steam vessels very advantageous. If the navigation of the gulf permits the Edith to be used she will answer, having both sails and steam. If she draws too much water, others of lighter draught could be procured. I mention this now, as the boundary commission will commence their labors on this end of the line, and will be on the Gila next season. I should have observed that the Colorado is supposed to be navigable only for boats drawing three or four feet.

I see no reason for posting troops on any other point out of reach of the ports on the Pacific. The Indians in the interior do not make it necessary, and it would be useless to place them near the mines to maintain order there. Nothing but the establishment of a regular civil government, to be carried on by those most interested in the existence of good order, will answer that end.

Such detachments as go to the southern part of the Territory will accordingly be placed, as heretofore mentioned, in healthy and convenient positions, and those on this bay at such points as will combine good climate, convenience of supply, and facility of movement. I propose, when such a point is found, to have removed all the public stores there, both from this place and Monterey, leaving the heavy ordnance and stores.

The town of San Francisco is no way fitted for military or commercial purposes; there is no harbor, a bad landing-place, bad water, no supplies of provisions, an inclement climate, and it is cut off from the rest of the country, except by a long circuit around the southern extremity of the bay. In time of war, enemies' troops could be landed for many miles south of the entrance of the bay on the sea beach, and thus cut it off by a short line across the peninsula on which it stands. There are points on the bay, more inland, having good harbors and landings, good water, and open to the whole country in rear, and accessible without difficulty to ships of the largest class. One of these should be the point at which the future depots should be established; and I propose to go to-morrow in the Edith, in company with Commodore Jones and other officers of the army and navy, to examine the straits of Karquinez, said to combine most advantages. I hope to return and report the result of our examination before the next mail boat leaves, (on Monday, 9th,) but at any rate by the succeeding boat, a few days afterwards.

I hope that in fixing the port of entry, capital, or other public places, the law will leave to the President the selection; otherwise, private interests already involved in speculation here, will, by misrepresentation, lead to a very bad choice.