Many owners - among an estimated 500,000 people forced to evacuate in the path of the fires - are desperately waiting to return home to tend to their animals.
Many were not allowed back into fire zones when they tried to return home with their empty horse trailers, after evacuating their first load.
The speed at which the fire spread forced many to evacuate so quickly, they had no opportunity to take their horses. They were either turned out in paddocks or even set free if owners felt they stood a better chance against the flames.
The strong Santa Ana winds have reportedly eased across California, but the fires continue to spread, having already destroyed 1500 buildings and burning through an estimated 165,000 hectares of countryside from Los Angeles to the Mexican border.
Many of the dozen or so blazes are expected to burn to the coast.
State officials estimate more than 165,000 homes are at threat from the fires. Five people have so far died.
San Diego County, with a dense horse population, is one of the worst affected areas in California. The Humane Society of the United States, at the request of the San Diego County Department of Animal Services, is helping in animal rescue efforts.
"The situation has become menacing for the residents and animals in the area," said Melissa Rubin, vice president of field services for The HSUS.
"Many residents were able to take their animals with them as they evacuated. Unfortunately, it is much harder to evacuate horses and farm animals."
More than 20 HSUS Disaster Services staff from across the country have been deployed to California to rescue horses, farm animals and pets affected by the rapidly advancing fires.
Across southern california, stables, fairgrounds and racecourses in safe areas are providing temporary homes for the equine evacuees. Some stables have nearly doubled their usual horse numbers to help out in the crisis.
Veterinarians are on standby to provide help for burnt and injured horses once people are allowed back into affected areas. Veterinary surgeries are ready to operate as treatment centres.
At the time of writing, the fire was reported to be burning through the heart of San Diego County, on a path for Del Mar racetrack, where 2000 evacuated horses are being held.
It is uncertain whether the horses will be moved again or whether firefighters will defend the course from the flames.
Other tracks such as Los Alamitos are also home to evacuated horses, having set up 180 additional stalls, made available on a first-come, first-served basis.
Qualcomm Stadium in San Diego was a temporary home to both people and animals, including horses.
Many local residents are inviting displaced people into their homes.
President George W. Bush has authorised federal aid for California. The military have been mobilised and the national guard has turned out to keep watch over evacuated homes.
States are now required to include pets in their disaster planning, as a result of the Hurricane Katrina disaster in New Orleans and the many thousands of pets that suffered in the aftermath.
Where possible, authorities try to keep pets and animals together.
A survey after Katrina showed that 61% of pet owners refused to evacuate without their animals.