San Francisco — ''Butterflies are not free,'' says E. Sherman Eubanks. He should know. Mr. Eubanks, president of Visitacion Associates, says the development firm spent some $1 million over the last two years in connection with research on the San Bruno Mountain habitat of three endangered butterfly subspecies. But that investment paid off in an agreement that will enable the company to go ahead with plans for $1 billion in commercial and residential construction on the sprawling, 1,315-foot-high mountain just south of San Francisco.
Some conservation groups and wildlife experts say Eubanks may have gotten a better bargain than the butterflies did. There is a possibility, according to one source, of a legal challenge.
Visitacion Associates had all its construction permits three years ago. Then it was discovered that the Mission Blue, San Bruno Elfin, and Callippe Silverspot butterflies - the first two on the endangered species list and the third a candidate for that status - had, in effect, prior claim to much of the mountain, which affords spectacular views of both the Pacific Ocean and San Francisco Bay.
That could have meant the end to development plans, except for an amendment to the 1973 Endangered Species Act permitting the kinds of trade-offs arranged by Visitacion Associates and the enforcement division of the US Fisheries and Wildlife Service.
The company financed a two-year study by Thomas Reid Associates, a Palo Alto, Calif., environmental consulting company. The result was a ''habitat conservation plan'' (HCP), approved March 9 by the Fisheries and Wildlife Service. Visitacion Associates will yield some of its land on San Bruno Mountain to the butterflies, but it will be permitted to ''take'' part of the insects' habitat in return for maintenance of the HCP.
An innovative feature of the plan provides for annual assessments of $20 on each home built and $10 on every 1,000 feet of commercial structures to provide some $60,000 a year for continued protection of the Mission Blue and Callippe Silverspot. These assessments, which will be paid by individual owners, would escalate with inflation.
Each development firm involved in the overall project will pay a portion of the $60,000 until its structures are built and sold, Mr. Eubanks explained. Until the structures they build are sold, developers involved in the project will collectively pay the $60,000.
Asked if the HCP assessments might have a negative impact on prospective buyers, Eubanks said he felt they would regard it as an acceptable price for having handy access to over 2,000 acres of scenic parkland.
About 80 percent of the mountainside is set aside for wildlife habitat - 2, 000 in parkland and 800 privately owned. Construction of houses and commercial buildings will begin in late summer on 372 acres owned by Visitacion Associates. Of some 273 acres owned by others, half will be set aside as part of the wildlife preserve and the rest will be open to eventual development.
Eubanks says total planned development by his group will take about 10 years.
Phil Lehenbauer, staff biologist for the Fisheries and Wildlife Service, points out that the San Bruno agreement involves ''recovery,'' not just protection for the endangered subspecies.
The Mission Blue is a tiny butterfly with dusty blue wings that measure about one inch from tip to tip; the wings' undersides are gray with black spots. The Callippe Silverspot is about twice as big; it has irregular wing stripes of black and tan, with silver spots on the light tan underside. The Reid study determined that the San Bruno Elfin would not be threatened by the planned development.
Richard Arnold, an entomolgist at the University of California-Berkeley who wrote his doctoral dissertation on the Mission Blue and Elfin, argues that the HCP will expose the butterflies to ''great risk.'' He charges that the Reid Associates study was not thorough enough and interpretation of findings was ''overly optimistic.''
Mr. Arnold also says the impact on 12 endangered plant species and some animals, including the rare San Francisco garter snake, was not given sufficient weight. A ''saddle'' area on the mountain, once owned by Visitacion Associates but since sold to the state, would have been a more acceptable site for development from the wildlife-preservation point of view, Arnold argues.
Thomas Reid defends the integrity of his study, saying objections such as Arnold's are politically inspired ''red herrings.''
After a dozen public hearings and lengthy review, the Fisheries and Wildlife Service decided to back Reid's recommendations.