MANAGUA, Nicaragua — Lisa A. Miller and her daughter, Isabella, started their fugitive lives here in the fall of 2009, disguised in the white scarves and long blue dresses of the Mennonites who spirited them out of the United States and adopting the aliases Sarah and Lydia.


Now 10, Isabella Miller-Jenkins has spent her last three birthdays on the run, “bouncing around the barrios of Nicaragua,” as one federal agent put it, a lively blond girl and her mother trying to blend in and elude the United States marshals who have traveled to the country in pursuit.


She can now chatter in Spanish, but her time in Nicaragua has often been lonely, those who have met her say, long on prayer but isolated. She has been told that she could be wrenched from her mother if they are caught. She has also been told that the other woman she once called “Mama,” Ms. Miller’s former partner from a civil union in Vermont that she has since renounced, cannot go to heaven because she lives in sin with women.


Isabella’s tumultuous life has embodied some of America’s bitterest culture wars — a choice, as Ms. Miller said in a courtroom plea, shortly before their desperate flight, “between two diametrically opposed worldviews on parentage and family.”


Isabella was 7 when she and Ms. Miller jumped into a car in Virginia, leaving behind their belongings and a family of pet hamsters to die without food or water. Supporters drove them to Buffalo, where they took a taxi to Canada and boarded a flight to Mexico and then Central America.


Ms. Miller, 44, is wanted by the F.B.I. and Interpol for international parental kidnapping. In their underground existence in this impoverished tropical country, she and Isabella have been helped by evangelical groups who endorse her decision to flee rather than to expose Isabella to the “homosexual lifestyle” of her other legal mother, Janet Jenkins.


In a tale filled with improbables, an Amish Mennonite sect known for simple living and avoiding politics has been drawn into the high-stakes criminal case: one of its pastors is facing trial in Vermont on Aug. 7 on charges of abetting the kidnapping.


The decade-long drama touches on some of the country’s most contentious social and legal questions, including the extension of civil union and marital rights to same-sex couples and what happens, in the courts and to children, when such unions dissolve.


In this case, the passions of any divorce were multiplied by Ms. Miller’s born-again conversion to conservative Christianity and her denouncing of lesbianism as an addiction. Ms. Miller repeatedly prevented Isabella’s court-ordered visits with Ms. Jenkins until an exasperated Vermont judge said he would transfer custody.


And then Ms. Miller fled.


Her supporters say she has been persecuted because of her religion. They made “Protect Isabella” a rallying cry at a time when more gay couples are raising children, whether through adoption or, in Lisa Miller’s case, in vitro fertilization.


“I only want to see my daughter,” Ms. Jenkins said in an interview this spring in the four-bedroom house in Vermont that she and Ms. Miller bought when they dreamed of having five children. Ms. Jenkins, 47, has since married another woman and runs a day care business.


Even as Ms. Miller disappeared with Isabella, the Vermont judge granted Ms. Jenkins formal custody of the girl, as of Jan. 1, 2010. Ms. Jenkins keeps a bedroom piled with toys that Isabella is surely outgrowing.


“What’s hard for me as a parent is not knowing what she’s going through,” Ms. Jenkins said.


At the center of the story is a girl, tall for her age, whose cheerful face appears on a poster from the National Center for Missing and Exploited Children. Based on the first extended interviews with the missionaries who harbored the pair, visits to places where Isabella and Ms. Miller stayed in Nicaragua and court documents, The New York Times has assembled the most complete picture yet of their getaway and subsequent life.


A Romance Turns Bitter