Clouds of bees bounce off a kitchen window in Chilmark. In Edgartown they cling together by the thousands and form a small pillow on the top of a house. This is bee swarming season, and apiarist Neil Flynn of West Tisbury has his hands full.

May and June are the busiest times for bees, according to Mr. Flynn. The flowers are in bloom and many bee colonies are on the move.

Early in May, Mr. Flynn, with the help of an assistant, removed a huge beehive from a precarious place at the Martha’s Vineyard Airport: bees had taken residence 30 feet up in the FAA tower.

“Honey was dripping down on the interior wall of the tower,” said Pete Nicol, a FAA technician involved in the case. He said the bees’ nest had been there for a few years.

“I don’t like doing this,” Mr. Flynn confessed last weekend as he removed three beehives from two homes, one in Edgartown and one in Chilmark, “because 90 per cent of the time it means I have to destroy the bees. The work is messy. It is hot. It is a terrible job.”

But for $450, he’ll come to a home and remove the bees from inside a wall, if the site isn’t too inconvenient to reach. Mr. Flynn does what no house carpenter wants to do, his hands extending into vacant cavities no one else wants to imagine.

People find bees residing in their home unnerving, more so even than finding other unwanted house guests — skunks, raccoons, squirrels. His customers are often hysterical with fright. Mr. Flynn described one customer: “She was freaking out.”

Take the couple in Edgartown, who were beside themselves explaining their situation on the phone; that is usually how it all starts.

“These folks had 20 pounds of honey and 50,000 bees in the wall, and they wanted me to get rid of them,” said Mr. Flynn, standing outside of their house on Friday.

Mr. Flynn is a calm soul in a world of hovering wings, stings and buzzing. “I don’t get excited anymore,” he said. He can recall one time his cool was tested: he said he was driving a truckload of bees and a deer jumped out in front of him.

At this time of year, bees in residence start getting restless. If the hive made it through the winter, they are preparing to split. Splitting is the natural process of one bee hive becoming two entirely separate hives, each with their own queen.

“The homeowner wonders why there is a chirping sound in the wall. Well, it is one queen bee calling out through the nest. She is letting all the other queens know she is there,” Mr. Flynn said.

(For the homeowner, it is one thing knowing there are bees behind the wallboard — but to hear them chirping is something else entirely.)

The hive at the Edgartown house was splitting. While Mr. Flynn was working at the Edgartown house, the second colony decided to leave the hive and it took flight. They formed a swarm at the peak of the house well above Mr. Flynn’s head.

The phenomenon is routine in nature, but still it has the effect of an Alfred Hitchcock film.

In Chilmark, Mr. Flynn’s assignment was a vacant summer home. It was thought initially there were two active colonies in the kitchen bay window, one above the window and one below the bay.

Evidence of the more than 50,000 bees was obvious. First, there was the loud sound of buzzing. Plus, there were hundreds of bees walking in and out of a very tiny entrance in the wall.

The Chilmark project required reenforcements; Mr. Flynn brought in his assistant, trainee Tyler R. Vunk, 31, of Edgartown.

On the scene, Mr. Vunk wrapped duct tape around his pant legs at the ankles. “I don’t want any surprises when I am driving,” he said. The two men put on bee jackets which included a screened mask.

Using steel scaffolding from Tilton Rentall, the men built a work platform right in front of the entryway to the buzzing hive. Even as they raised the scaffolding, the bees began swirling around the entrance.

To the layman, all bees seem ferocious. But there are differences.

“You never know what kind of bees you are dealing with until you start,” Mr. Flynn said. “There is a Russian hybrid of bees that tends to be a little aggressive.”

Mr. Vunk laughed at the words “a little aggressive.” He said his colleague was a true New Englander in the way he tends to understate. Describing bees as being “a little aggressive” means that they will sting, sting, sting, Mr. Vunk said.

Mr. Flynn starts a small fire in the “smoker,” a medium-sized tin can that looks like a cross between a can and the head of the Tin Man in the Wizard of Oz. The smoke comes out the top. And using finger-operated bellows on the side, smoke can be blown right into the entrance of the hive.

The smoke interferes with the bees’ usual instinct to defend the hive. It makes the bees turn their attention to the honey in the hive and away from the appearance of an intruder.

Once inside the walls of the kitchen, Mr. Flynn discovers that the hive under the bay window is dead. Though there is an extensive array of honeycomb and still available honey, there are no bees.

Mr. Flynn takes the remains of the hive and fills a five-gallon bucket.

The hive above the bay window is a far more hearty colony. Mr. Flynn calls these bees docile, and adds they must be an Italian strain.

When the two men pull a plank off the roof of the bay window, the full size of the hive becomes apparent. It reaches deep into the house. It is huge.

Bees form a fog over the two men, as Mr. Flynn methodically reaches in and takes out pieces of the hive. The buzzing sound is considerably louder.

Taking out the honeycomb, Mr. Flynn appears as though he is taking pages from a large yellow phonebook. The bees walk over the sticky comb undisturbed. Mr. Flynn puts the remains of the hive into buckets and a box.

Mr. Flynn’s enthusiasm for the work shows when he finds the hive’s most important resident. “I found the queen,” he called. He takes the honeycomb with the queen and gives it a special place in a wooden box.

Bees without their queen will die, and Mr. Flynn is trying to make this an act of kindness and not an act entirely of destruction.

Several five-gallon buckets are filled.

Mr. Vunk grabs the Eureka (“The Boss”) vacuum cleaner and starts sucking up all the errant bees in the area. The two men, the loud vacuum cleaner and the buzzing are like a scene out of Ghostbusters; Mr. Vunk said he knows the movie well.

“I wait tables at Zephrus restaurant. It is a little bit more mellow there,” Mr. Vunk said.

The work on Saturday went a lot more quickly than some past projects. Mr. Flynn said removing a honey beehive at the Martha’s Vineyard Airport took more effort. The hive was 30 feet up on the tower. The staging was complicated. Plus, here were Homeland Security forces hovering over Mr. Flynn’s work.

“That was a big hive,” Mr. Flynn recalled, with that understatement again.

Bees around the world are in trouble, and there is just as much trouble here on the Vineyard. Though this time of year would suggest there are a lot of hives on the Island, bees are struggling through difficult times.

Mr. Flynn said if he could find a bee colony that would last from year to year, he could be a rich man. A parasitic mite is killing bees and hives. It is not just an issue for those who want to produce lots of honey. Pollination is the key ingredient to a healthy home garden and a productive farm; bees are essential.

Mr. Flynn runs Katama Apiary, a commercial honey operation that has been producing gallons of honey every year since 1994. He shares his work with his partner, Jacquie Balaschak.

Their honey is available at the farmers’ market, Morning Glory Farm and at both Cronig’s markets.

“I try to operate at least 100 hives,” he said. He has hives in West Tisbury, Chilmark and Edgartown.

Many of those bees are new, however, purchased from off-Island. “This year we brought in 30 queens, 30 colonies and ended up with 60 hives out there,” he said. He uses the process of splitting hives from one to two, from two to four.

“Bees have all kinds of problems. Beekeeping has changed dramatically in just the past 10 years,” Mr. Flynn said. “It used to be, you could keep a hive of bees in the backyard and they’d last for ever. Now you’ve got to watch them all the time. They have to be [well] treated. If you get a couple of seasons from a hive you are doing well,” he said.

Bee swarming season on the Vineyard runs from May 15 to June 15, though there are exceptions. On the last day of June in 1983, a swarm of tens of thousands of bees held up car and boat traffic at the Steamship Authority wharf in Oak Bluffs for hours until members of the Dunkl family came in and removed the bees.

It can create home hazards as well.“It takes a strong woman to stand behind a man with bees,” said Ms. Balaschak. “I am always scraping beeswax off the kitchen floor.”